5L0K - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF AUTOTAXIN AND COMPOUND PF-8380

Authors :   J. D. Durbin

Date :   27 Jul 16 (Deposition) - 10 Aug 16 (Release) - 05 Oct 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.73

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Phospholipase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. B. Jones, L. A. Pfeifer, T. J. Bleisch, T. J. Beauchamp, J. D. Durbin, V. J. Klimkowski, N. E. Hughes, C. J. Rito, Y. Dao, J. M. Gruber, H. Bui, M. G. Chambers, S. Chandrasekhar, C. Lin, D. J. Mccann, D. R. Mudra, J. L. Oskins, C. A. Swearingen, K. Thirunavukkarasu, B. H. Norman
Novel Autotaxin Inhibitors For The Treatment Of Osteoarthritis Pain: Lead Optimization Via Structure-Based Drug Design.
Acs Med. Chem. Lett. V. 7 857 2016
PubMed-ID: 27660691 | Reference-DOI: 10.1021/ACSMEDCHEMLETT.6B00207

Molecule 1 - ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE FAMILY MEMBER 2
	Chains	:	A, B
	EC Number	:	3.1.4.39
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Common	:	HUMAN
	Expression System Taxid	:	9606
	Fragment	:	UNP RESIDUES 51-859
	Gene	:	ENPP2, ATX, NPPS2
	Organism Common	:	RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	E-NPP 2,AUTOTAXIN,EXTRACELLULAR LYSOPHOSPHOLIPASE D,LYSOPLD

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (7, 17)

No.	Name	Count	Type	Full Name
1	6ZO	2	Ligand/Ion	(3,5-DICHLOROPHENYL)METHYL 4-[3-OXO-3-(2-OXO-2,3-DIHYDRO-1,3-BENZOXAZOL-6-YL)PROPYL]PIPERAZINE-1-CARBOXYLATE
2	BMA	1	Ligand/Ion	BETA-D-MANNOSE
3	CA	2	Ligand/Ion	CALCIUM ION
4	CL	2	Ligand/Ion	CHLORIDE ION
5	EPE	2	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
6	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
7	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	6ZO	1	Ligand/Ion	(3,5-DICHLOROPHENYL)METHYL 4-[3-OXO-3-(2-OXO-2,3-DIHYDRO-1,3-BENZOXAZOL-6-YL)PROPYL]PIPERAZINE-1-CARBOXYLATE
2	BMA	-1	Ligand/Ion	BETA-D-MANNOSE
3	CA	-1	Ligand/Ion	CALCIUM ION
4	CL	-1	Ligand/Ion	CHLORIDE ION
5	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
6	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
7	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (4, 5)

No.	Name	Count	Type	Full Name
1	6ZO	1	Ligand/Ion	(3,5-DICHLOROPHENYL)METHYL 4-[3-OXO-3-(2-OXO-2,3-DIHYDRO-1,3-BENZOXAZOL-6-YL)PROPYL]PIPERAZINE-1-CARBOXYLATE
2	BMA	1	Ligand/Ion	BETA-D-MANNOSE
3	CA	-1	Ligand/Ion	CALCIUM ION
4	CL	-1	Ligand/Ion	CHLORIDE ION
5	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
6	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
7	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:311 , HIS A:315 , HIS A:474 , 6ZO A:906	binding site for residue ZN A 903
02	AC2	SOFTWARE	ASP A:171 , THR A:209 , ASP A:358 , HIS A:359	binding site for residue ZN A 904
03	AC3	SOFTWARE	ASP A:739 , ASN A:741 , ASP A:743 , LEU A:745 , ASP A:747	binding site for residue CA A 905
04	AC4	SOFTWARE	ASP A:171 , THR A:209 , LEU A:213 , ALA A:217 , PHE A:273 , PHE A:274 , TRP A:275 , TYR A:306 , ASP A:311 , HIS A:315 , HIS A:474 , ZN A:903 , HOH A:1027 , PHE B:777	binding site for residue 6ZO A 906
05	AC5	SOFTWARE	ASP A:146 , CYS A:148 , GLU A:149 , LYS A:190 , HIS A:348 , ARG A:349 , TYR A:490	binding site for residue EPE A 907
06	AC6	SOFTWARE	GLY A:229 , ASN A:230 , SER A:231 , ARG A:391	binding site for residue CL A 908
07	AC7	SOFTWARE	ASP B:311 , HIS B:315 , HIS B:474 , 6ZO B:907	binding site for residue ZN B 904
08	AC8	SOFTWARE	ASP B:171 , THR B:209 , ASP B:358 , HIS B:359	binding site for residue ZN B 905
09	AC9	SOFTWARE	ASP B:739 , ASN B:741 , ASP B:743 , LEU B:745 , ASP B:747	binding site for residue CA B 906
10	AD1	SOFTWARE	PHE A:777 , ASP B:171 , THR B:209 , LEU B:213 , ALA B:217 , PHE B:273 , PHE B:274 , TRP B:275 , TYR B:306 , ASP B:311 , HIS B:315 , HIS B:474 , ZN B:904	binding site for residue 6ZO B 907
11	AD2	SOFTWARE	CYS B:148 , GLU B:149 , LYS B:190 , HIS B:348 , ARG B:349 , TYR B:490	binding site for residue EPE B 908
12	AD3	SOFTWARE	ASN B:230 , SER B:231 , ARG B:391	binding site for residue CL B 909
13	AD4	SOFTWARE	LEU A:220 , PRO A:522 , ASN A:524 , HOH A:1002	binding site for Poly-Saccharide residues NAG A 901 through NAG A 902 bound to ASN A 524
14	AD5	SOFTWARE	HIS B:433 , PRO B:522 , ASN B:524 , LEU B:745 , HIS B:831	binding site for Poly-Saccharide residues NAG B 901 through BMA B 903 bound to ASN B 524

Asymmetric Unit

No.	Residues
1	A:58	-	A:75
2	A:62	-	A:93
3	A:73	-	A:86
4	A:79	-	A:85
5	A:102	-	A:119
6	A:107	-	A:137
7	A:117	-	A:130
8	A:123	-	A:129
9	A:148	-	A:194
10	A:156	-	A:350
11	A:366	-	A:468
12	A:413	-	A:805
13	A:566	-	A:666
14	A:568	-	A:651
15	A:774	-	A:784
16	B:58	-	B:75
17	B:62	-	B:93
18	B:73	-	B:86
19	B:79	-	B:85
20	B:102	-	B:119
21	B:107	-	B:137
22	B:117	-	B:130
23	B:123	-	B:129
24	B:148	-	B:194
25	B:156	-	B:350
26	B:366	-	B:468
27	B:413	-	B:805
28	B:566	-	B:666
29	B:568	-	B:651
30	B:774	-	B:784

Asymmetric Unit

No.	Residues
1	Pro A:70	-	Pro A:71
2	Tyr A:205	-	Pro A:206
3	Gln A:309	-	Pro A:310
4	Gly B:69	-	Pro B:70
5	Pro B:70	-	Pro B:71
6	Tyr B:205	-	Pro B:206
7	Gln B:309	-	Pro B:310

(no "SAP(SNP)/Variant" information available for 5L0K)

(no "PROSITE Motif" information available for 5L0K)

(no "Exon" information available for 5L0K)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:777
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................................hhhhhhh...........................hhhhhh....hhhhhh....hhhhh..................eeeeeee....hhhhhhhhhhhhhhhhhhhhee...ee.....hhhhhhhhhhhh.hhhhhh.....eee....eee....hhhhhhhhh...hhhhhhhhh.............hhhhhhhhhhhhhh........eeeeeeeeehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee....ee.....eee.hhh..hhh.eeee....eeeee........hhhhhhhhhh.......eeeee.hhhhhhhh.........eeeee....eee.......ee......hhhhh..eeee.......ee...ee..hhhhhhhhhhh............hhhhh.......................hhhhh.........hhhhh.....ee.....eeeee....eeeee....eeeeeeeee.........hhhhh.........hhhhh.hhhhhhhh...eeee..hhhhh.hhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee..........hhhhh.............eeeeeeeee.....hhhhh...eeeeeeeee.............hhhhhhhhhhhhheehhhhhhhhhhee.......hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l0k A  53 ATSGSCKGRCFELQEVGPPDCRCDNLCKSYSSCCHDFDELCLKTARGWECTKDRCGEVRNEENACHCSEDCLSRGDCCTNYQVVCKGESHWVDDDCEEIKVPECPAGFVRPPLIIFSVDGFRASYMKKGSKVMPNIEKLRSCGTHAPYMRPVYPTKTFPNLYTLATGLYPESHGIVGNSMYDPVFDASFHLRGREKFNHRWWGGQPLWITATKQGVRAGTFFWSVSIPHERRILTILQWLSLPDNERPSVYAFYSEQPDFSGHKYGPFGPEMTNPLREIDKTVGQLMDGLKQLRLHRCVNVIFVGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRAKSIANSKYDPKTIIAALTCKKPDQHFKPYMKQHLPKRLHYANNRRIEDIHLLVDRRWHVARKPCFFQGDHGFDNKVNSMQTVFVGYGPTFKYRTKVPPFENIELYNVMCDLLGLKPAPNNGTHGSLNHLLRTNTFRPTMPDEVSRPNYPGIMYLQSEFDLGCTCDDTEERHLLYGRPAVLYRTSYDILYHTDFESGYSEIFLMPLWTSYTISKQAEVSSIPEHLTNCVRPDVRVSPGFSQNCLAYKNDKQMSYGFLFPPYLSSSPEAKYDAFLVTNMVPMYPAFKRVWAYFQRVLVKKYASERNGVNVISGPIFDYNYDGLRDTEDEIKQYVEGSSIPVPTHYYSIITSCLDFTQPADKCDGPLSVSSFILPHRPDNDESCASSEDESKWVEELMKMHTARVRDIEHLTGLDFYRKTSRSYSEILTLKTYLHTYE 859
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452    || 472       482       492       502       512       522       532       542       552       562       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       
                                                                                                                                                                                                                                                                                                                                                                                                                                              457|                                                                                                   570|                                                                                                                                                                                                                                                                            
                                                                                                                                                                                                                                                                                                                                                                                                                                               468                                                                                                    591

Chain B from PDB  Type:PROTEIN  Length:777
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh...............................hhhhhhh...........................hhhhhh....hhhhhhh..........................eeeeeee..hhhhh...hhhhhhhhhhhee...ee.....hhhhhhhhhhhh.hhhhhh.....eee....eee....hhhhhhhhh...hhhhhhhhh.............hhhhhhhhhhhhhh........eeeeeeeeehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee...........eee.hhh..hhh.eeee....eeeee........hhhhhhhhhh.......eeeee.hhhhhhhh.........eeeee....eee..................hhhhh..eeee.......ee...ee..hhhhhhhhhh.............hhhhh.......................hhhhh........hhhhh.....ee.....eeeee....eeeee....eeeeeeeee.........hhhhh...............hhhhhhhh...eeee..hhhhh....hhhhhh....eeeehhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee..........hhhhh.............eeeeeeeee.....hhhhh...eeeeeeeee.............hhhhhhhhhhhhheehhhhhhhhhhee.......hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l0k B  52 TATSGSCKGRCFELQEVGPPDCRCDNLCKSYSSCCHDFDELCLKTARGWECTKDRCGEVRNEENACHCSEDCLSRGDCCTNYQVVCKGESHWVDDDCEEIKVPECPAGFVRPPLIIFSVDGFRASYMKKVMPNIEKLRSCGTHAPYMRPVYPTKTFPNLYTLATGLYPESHGIVGNSMYDPVFDASFHLRGREKFNHRWWGGQPLWITATKQGVRAGTFFWSVSIPHERRILTILQWLSLPDNERPSVYAFYSEQPDFSGHKYGPFGPEMTNPLREIDKTVGQLMDGLKQLRLHRCVNVIFVGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRAKSIANSKYDPKTIIAALTCKKPDQHFKPYMKQHLPKRLHYANNRRIEDIHLLVDRRWHVARKPLDVCFFQGDHGFDNKVNSMQTVFVGYGPTFKYRTKVPPFENIELYNVMCDLLGLKPAPNNGTHGSLNHLLRTNTFRPTMPDEVSRPNYPGIMYLQSEFDLGCTCDTEERHLLYGRPAVLYRTSYDILYHTDFESGYSEIFLMPLWTSYTISKQAEVSSIPEHLTNCVRPDVRVSPGFSQNCLAYKNDKQMSYGFLFPPYLSSSPEAKYDAFLVTNMVPMYPAFKRVWAYFQRVLVKKYASERNGVNVISGPIFDYNYDGLRDTEDEIKQYVEGSSIPVPTHYYSIITSCLDFTQPADKCDGPLSVSSFILPHRPDNDESCASSEDESKWVEELMKMHTARVRDIEHLTGLDFYRKTSRSYSEILTLKTYLHTYE 859
                                    61        71        81        91       101       111       121       131       141       151       161       171       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454     ||471       481       491       501       511       521       531       541       551       561       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       
                                                                                                                                                         179|                                                                                                                                                                                                                                                                                  460|                                                                                                  569|                                                                                                                                                                                                                                                                            
                                                                                                                                                          183                                                                                                                                                                                                                                                                                   468                                                                                                   591

Legend:		→ Mismatch	(orange background)
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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 5L0K)

(no "CATH Domain" information available for 5L0K)

(no "Pfam Domain" information available for 5L0K)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		6ZO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Cis Peptide Bonds
		Gln A:309 - Pro A:310	[ RasMol ]
		Gln B:309 - Pro B:310	[ RasMol ]
		Gly B:69 - Pro B:70	[ RasMol ]
		Pro A:70 - Pro A:71	[ RasMol ]
		Pro B:70 - Pro B:71	[ RasMol ]
		Tyr A:205 - Pro A:206	[ RasMol ]
		Tyr B:205 - Pro B:206	[ RasMol ]

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		Biological Unit 2	[ Jena3D ]

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	5l0k
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	ENPP2_RAT \| Q64610
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	3.1.4.39
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UniProtKB/Swiss-Prot
	ENPP2_RAT \| Q64610	:	2xr9 2xrg 5dlt 5dlv 5dlw 5ijq 5ijs 5l0b 5l0e 5lqq

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 17)

Sites (14, 14)

SS Bonds (30, 30)

Cis Peptide Bonds (7, 7)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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