5U7K - JenaLib

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Biological Unit 4 (Jmol Viewer)

Title :   PDE2 CATALYTIC DOMAIN COMPLEXED WITH INHIBITORS

Authors :   J. Pandit, K. Parris

Date :   12 Dec 16 (Deposition) - 28 Jun 17 (Release) - 28 Jun 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.06

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Pde2, Sbdd, Inhibitor, Phosphodiesterase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. J. Helal, E. P. Arnold, T. L. Boyden, C. Chang, T. A. Chappie, K. F. Fennell, M. D. Forman, M. Hajos, J. F. Harms, W. E. Hoffmann, J. M. Humphrey, Z. Kang, R. J. Kleiman, B. L. Kormos, C. W. Lee, J. Lu, N. Maklad, L. Mcdowell, S. Mente, R. E. O'Connor, J. Pandit, M. Piotrowski, A. W. Schmidt, C. J. Schmidt, H. Ueno, P. R. Verhoest, E. X. Yang
Application Of Structure-Based Design And Parallel Chemistr To Identify A Potent, Selective, And Brain Penetrant Phosphodiesterase 2A Inhibitor.
J. Med. Chem. 2017
PubMed-ID: 28574706 | Reference-DOI: 10.1021/ACS.JMEDCHEM.7B00397

Molecule 1 - CGMP-DEPENDENT 3',5'-CYCLIC PHOSPHODIESTERASE
	Chains	:	A, B, C, D
	EC Number	:	3.1.4.17
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Strain	:	SF21
	Expression System Taxid	:	7108
	Fragment	:	CATALYTIC DOMAIN OF PDE2, UNP RESIDUES 323-663
	Gene	:	PDE2A
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CYCLIC GMP-STIMULATED PHOSPHODIESTERASE,CGSPDE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 13)

No.	Name	Count	Type	Full Name
1	7Y1	4	Ligand/Ion	3-[5-(4-ETHYLPHENYL)-1-METHYL-1H-PYRAZOL-4-YL]-5-PROPOXY[1,2,4]TRIAZOLO[4,3-A]PYRAZINE
2	CL	1	Ligand/Ion	CHLORIDE ION
3	MG	4	Ligand/Ion	MAGNESIUM ION
4	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	7Y1	1	Ligand/Ion	3-[5-(4-ETHYLPHENYL)-1-METHYL-1H-PYRAZOL-4-YL]-5-PROPOXY[1,2,4]TRIAZOLO[4,3-A]PYRAZINE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	7Y1	1	Ligand/Ion	3-[5-(4-ETHYLPHENYL)-1-METHYL-1H-PYRAZOL-4-YL]-5-PROPOXY[1,2,4]TRIAZOLO[4,3-A]PYRAZINE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	7Y1	1	Ligand/Ion	3-[5-(4-ETHYLPHENYL)-1-METHYL-1H-PYRAZOL-4-YL]-5-PROPOXY[1,2,4]TRIAZOLO[4,3-A]PYRAZINE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	7Y1	1	Ligand/Ion	3-[5-(4-ETHYLPHENYL)-1-METHYL-1H-PYRAZOL-4-YL]-5-PROPOXY[1,2,4]TRIAZOLO[4,3-A]PYRAZINE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:660 , HIS A:696 , ASP A:697 , ASP A:808 , HOH A:1106 , HOH A:1142	binding site for residue ZN A 1001
02	AC2	SOFTWARE	ASP A:697 , HOH A:1101 , HOH A:1106 , HOH A:1144 , HOH A:1178 , HOH A:1182	binding site for residue MG A 1002
03	AC3	SOFTWARE	LEU A:770 , ASP A:808 , ILE A:826 , PHE A:830 , GLN A:859 , PHE A:862 , HOH A:1132 , HOH A:1162 , HOH A:1199	binding site for residue 7Y1 A 1003
04	AC4	SOFTWARE	HIS B:660 , HIS B:696 , ASP B:697 , ASP B:808 , HOH B:1168 , HOH B:1173	binding site for residue ZN B 1001
05	AC5	SOFTWARE	ASP B:697 , HOH B:1113 , HOH B:1126 , HOH B:1168 , HOH B:1185 , HOH B:1191	binding site for residue MG B 1002
06	AC6	SOFTWARE	LEU B:770 , ASP B:808 , LEU B:809 , ILE B:826 , PHE B:830 , GLN B:859 , PHE B:862 , HOH B:1135 , HOH B:1162 , HOH B:1178	binding site for residue 7Y1 B 1003
07	AC7	SOFTWARE	HIS C:660 , HIS C:696 , ASP C:697 , ASP C:808 , HOH C:1132 , HOH C:1178	binding site for residue ZN C 1001
08	AC8	SOFTWARE	ASP C:697 , HOH C:1129 , HOH C:1131 , HOH C:1132 , HOH C:1157 , HOH C:1184	binding site for residue MG C 1002
09	AC9	SOFTWARE	ALA C:717 , SER C:720 , SER C:721 , ARG D:762	binding site for residue CL C 1003
10	AD1	SOFTWARE	LEU C:770 , HIS C:773 , THR C:805 , ASP C:808 , LEU C:809 , ILE C:826 , PHE C:830 , GLN C:859 , PHE C:862 , HOH C:1137 , HOH C:1168 , HOH C:1211	binding site for residue 7Y1 C 1004
11	AD2	SOFTWARE	HIS D:660 , HIS D:696 , ASP D:697 , ASP D:808 , HOH D:1109 , HOH D:1140	binding site for residue ZN D 1001
12	AD3	SOFTWARE	ASP D:697 , HOH D:1108 , HOH D:1109 , HOH D:1118 , HOH D:1121 , HOH D:1194	binding site for residue MG D 1002
13	AD4	SOFTWARE	LEU D:770 , HIS D:773 , THR D:805 , ASP D:808 , PHE D:830 , GLN D:859 , PHE D:862 , HOH D:1113 , HOH D:1163 , HOH D:1178	binding site for residue 7Y1 D 1003

(no "SS Bond" information available for 5U7K)

(no "Cis Peptide Bond" information available for 5U7K)

(no "SAP(SNP)/Variant" information available for 5U7K)

(no "PROSITE Motif" information available for 5U7K)

(no "Exon" information available for 5U7K)

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:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh....hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u7k A 577 AMDDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFL 916
                                   586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896       906       916

Chain B from PDB  Type:PROTEIN  Length:343
                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u7k B 576 SAMDDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLDE 918
                                   585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915

Chain C from PDB  Type:PROTEIN  Length:339
                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.........hhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u7k C 580 DEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLDE 918
                                   589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909

Chain D from PDB  Type:PROTEIN  Length:327
                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5u7k D 590 IQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFL 916
                                   599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909

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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 5U7K)

(no "CATH Domain" information available for 5U7K)

(no "Pfam Domain" information available for 5U7K)

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	5u7k
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Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (4, 13)

Sites (13, 13)

SS Bonds (0, 0)

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