4O9S - JenaLib

Title :   CRYSTAL STRUCTURE OF RETINOL-BINDING PROTEIN 4 (RBP4)IN COMPLEX WITH A NON-RETINOID LIGAND

Authors :   Z. Wang, S. Johnstone, N. P. Walker

Date :   02 Jan 14 (Deposition) - 02 Jul 14 (Release) - 02 Jul 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A (1x),B (1x)

Keywords :   Retinol Binding, Disease Mutation, Retinol-Binding, Secreted, Sensory Transduction, Transport, Vision, Vitamin A, Transport Protein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Wang, R. Connors, P. Fan, X. Wang, Z. Wang, J. Liu, F. Kayser, J. C. Medina, S. Johnstone, H. Xu, S. Thibault, N. Walker, M. Conn, Y. Zhang, Q. Liu, M. P. Grillo, A. Motani, P. Coward, Z. Wang
Structure-Assisted Discovery Of The First Non-Retinoid Ligands For Retinol-Binding Protein 4.
Bioorg. Med. Chem. Lett. V. 24 2885 2014
PubMed-ID: 24835984 | Reference-DOI: 10.1016/J.BMCL.2014.04.089

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 32)

Asymmetric Unit (4, 32)

No.	Name	Count	Type	Full Name
1	2RY	2	Ligand/Ion	1-[4-(8LAMBDA~4~-CYCLOPENTA[4,5]THIENO[2,3-D]PYRIMIDIN-4-YL)PIPERAZIN-1-YL]-2-[2-(TRIFLUOROMETHYL)PHENYL]ETHANONE
2	CL	3	Ligand/Ion	CHLORIDE ION
3	EDO	26	Ligand/Ion	1,2-ETHANEDIOL
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 1 (3, 15)

No.	Name	Count	Type	Full Name
1	2RY	1	Ligand/Ion	1-[4-(8LAMBDA~4~-CYCLOPENTA[4,5]THIENO[2,3-D]PYRIMIDIN-4-YL)PIPERAZIN-1-YL]-2-[2-(TRIFLUOROMETHYL)PHENYL]ETHANONE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EDO	13	Ligand/Ion	1,2-ETHANEDIOL
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 2 (2, 14)

No.	Name	Count	Type	Full Name
1	2RY	1	Ligand/Ion	1-[4-(8LAMBDA~4~-CYCLOPENTA[4,5]THIENO[2,3-D]PYRIMIDIN-4-YL)PIPERAZIN-1-YL]-2-[2-(TRIFLUOROMETHYL)PHENYL]ETHANONE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EDO	13	Ligand/Ion	1,2-ETHANEDIOL
4	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 3 (3, 15)

No.	Name	Count	Type	Full Name
1	2RY	1	Ligand/Ion	1-[4-(8LAMBDA~4~-CYCLOPENTA[4,5]THIENO[2,3-D]PYRIMIDIN-4-YL)PIPERAZIN-1-YL]-2-[2-(TRIFLUOROMETHYL)PHENYL]ETHANONE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EDO	13	Ligand/Ion	1,2-ETHANEDIOL
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Sites (31, 31)

Asymmetric Unit (31, 31)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LEU A:35 , PHE A:36 , LEU A:37 , ALA A:55 , ALA A:57 , MET A:73 , VAL A:74 , GLY A:75 , MET A:88 , TYR A:90 , ASP A:102 , ARG A:121 , TYR A:133 , PHE A:135 , HOH A:303	BINDING SITE FOR RESIDUE 2RY A 201
02	AC2	SOFTWARE	GLU A:81 , ASP A:82	BINDING SITE FOR RESIDUE EDO A 202
03	AC3	SOFTWARE	PHE A:9 , ARG A:10 , VAL A:107 , ARG A:155 , GLU A:158 , EDO A:211	BINDING SITE FOR RESIDUE EDO A 203
04	AC4	SOFTWARE	ASP A:126 , LEU A:144 , HOH A:311	BINDING SITE FOR RESIDUE EDO A 204
05	AC5	SOFTWARE	THR A:80 , GLU A:81	BINDING SITE FOR RESIDUE EDO A 205
06	AC6	SOFTWARE	GLN A:156 , ARG A:163 , TYR A:165	BINDING SITE FOR RESIDUE EDO A 206
07	AC7	SOFTWARE	VAL A:42 , THR A:56 , ALA A:57 , LYS A:58	BINDING SITE FOR RESIDUE EDO A 207
08	AC8	SOFTWARE	ASP A:31 , GLN A:164 , ARG A:166	BINDING SITE FOR RESIDUE EDO A 208
09	AC9	SOFTWARE	LYS A:30 , ASP A:31 , PRO A:32 , GLU A:33 , ALA A:130 , ASP A:131 , SER A:132	BINDING SITE FOR RESIDUE EDO A 209
10	BC1	SOFTWARE	VAL A:42 , HIS A:170 , ASN A:171 , GLY A:172	BINDING SITE FOR RESIDUE EDO A 210
11	BC2	SOFTWARE	ARG A:10 , VAL A:11 , VAL A:107 , ARG A:155 , EDO A:203 , HOH A:313	BINDING SITE FOR RESIDUE EDO A 211
12	BC3	SOFTWARE	ASN A:142 , HIS A:170 , PEG A:217 , HOH A:354	BINDING SITE FOR RESIDUE EDO A 212
13	BC4	SOFTWARE	ASN A:66 , TRP A:67 , LEU B:35 , 2RY B:201	BINDING SITE FOR RESIDUE EDO A 213
14	BC5	SOFTWARE	TRP A:91 , TRP B:91 , EDO B:209 , HOH B:398	BINDING SITE FOR RESIDUE EDO A 214
15	BC6	SOFTWARE	ASP A:72 , ALA A:94 , SER A:95 , PHE A:96	BINDING SITE FOR RESIDUE CL A 215
16	BC7	SOFTWARE	TRP B:67	BINDING SITE FOR RESIDUE CL A 216
17	BC8	SOFTWARE	ASP A:103 , CYS A:120 , HIS A:170 , ASN A:171 , EDO A:212 , HOH A:400	BINDING SITE FOR RESIDUE PEG A 217
18	BC9	SOFTWARE	EDO A:213 , LEU B:35 , PHE B:36 , LEU B:37 , ALA B:55 , ALA B:57 , VAL B:61 , MET B:73 , VAL B:74 , GLY B:75 , MET B:88 , TYR B:90 , ASP B:102 , ARG B:121 , TYR B:133 , PHE B:135 , HOH B:307	BINDING SITE FOR RESIDUE 2RY B 201
19	CC1	SOFTWARE	GLU A:13 , ASN A:14 , PRO B:145 , GLU B:147	BINDING SITE FOR RESIDUE EDO B 202
20	CC2	SOFTWARE	PHE B:9 , ARG B:10 , VAL B:107 , ARG B:155 , GLU B:158	BINDING SITE FOR RESIDUE EDO B 203
21	CC3	SOFTWARE	ASP B:3	BINDING SITE FOR RESIDUE EDO B 204
22	CC4	SOFTWARE	ARG B:10 , VAL B:11 , LYS B:12 , VAL B:107 , ASP B:108 , ARG B:155 , HOH B:318	BINDING SITE FOR RESIDUE EDO B 205
23	CC5	SOFTWARE	ASP B:103 , CYS B:120 , LEU B:123 , VAL B:169 , HIS B:170 , EDO B:210 , EDO B:214	BINDING SITE FOR RESIDUE EDO B 206
24	CC6	SOFTWARE	LYS B:30 , ASP B:31 , GLN B:164 , HOH B:394	BINDING SITE FOR RESIDUE EDO B 207
25	CC7	SOFTWARE	LYS B:87 , ASN B:101 , ASP B:102 , ASP B:103 , ASN B:171 , EDO B:213 , EDO B:214	BINDING SITE FOR RESIDUE EDO B 208
26	CC8	SOFTWARE	LEU A:97 , EDO A:214 , TRP B:91 , GLY B:92 , LEU B:97 , GLN B:98 , HOH B:341	BINDING SITE FOR RESIDUE EDO B 209
27	CC9	SOFTWARE	LEU B:123 , PRO B:141 , ASN B:142 , HIS B:170 , EDO B:206 , EDO B:214 , HOH B:368 , HOH B:411	BINDING SITE FOR RESIDUE EDO B 210
28	DC1	SOFTWARE	ARG B:153 , GLN B:156 , ARG B:163 , GLN B:164 , TYR B:165 , HOH B:326	BINDING SITE FOR RESIDUE EDO B 212
29	DC2	SOFTWARE	ASN B:101 , ASP B:102 , ARG B:121 , VAL B:169 , ASN B:171 , EDO B:208 , HOH B:343	BINDING SITE FOR RESIDUE EDO B 213
30	DC3	SOFTWARE	LYS B:87 , ASP B:103 , HIS B:170 , ASN B:171 , EDO B:206 , EDO B:208 , EDO B:210	BINDING SITE FOR RESIDUE EDO B 214
31	DC4	SOFTWARE	ASP B:72 , ALA B:94 , SER B:95 , PHE B:96	BINDING SITE FOR RESIDUE CL B 215

SS Bonds (6, 6)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

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

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Chain A from PDB  Type:PROTEIN  Length:175
                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhheeeeeeeee........eeeeeeeee.....eeeeeeeeee.....eeeeeeeeeeee.....eeeeeeee......eeeeeeeeeee....eeeeeeeeee.....eeeeeeeeee......hhhhhhhhhhhhhhh......ee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o9s A   1 ERDCRVSSFRVKENFDKARFSGTWYAMAKKDPEGLFLQDNIVAEFSVDETGQMSATAKGRVRLLNNWDVCADMVGTFTDTEDPAKFKMKYWGVASFLQKGNDDHWIVDTDYDTYAVQYSCRLLNLDGTCADSYSFVFSRDPNGLPPEAQKIVRQRQEELCLARQYRLIVHNGYCD 175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

Chain B from PDB  Type:PROTEIN  Length:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhh......hhhhhheeeeeeeee........eeeeeeeee.....eeeeeeeeeeee..eeeeeeeeeeeee.....eeeeeeee......eeeeeeeeeee....eeeeeeeeee.....eeeeeeeeee......hhhhhhhhhhhhhhh......ee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4o9s B   1 ERDCRVSSFRVKENFDKARFSGTWYAMAKKDPEGLFLQDNIVAEFSVDETGQMSATAKGRVRLLNNWDVCADMVGTFTDTEDPAKFKMKYWGVASFLQKGNDDHWIVDTDYDTYAVQYSCRLLNLDGTCADSYSFVFSRDPNGLPPEAQKIVRQRQEELCLARQYRLIVHNGYC 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

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Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (39, 39)

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