5TZC - JenaLib

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Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN PDE2A IN COMPLEX WITH (5S)-1-[(3-BROMO-4-FLUOROPHENYL)CARBONYL]-3,3-DIFLUORO-5-{5-METHYL-[1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7-YL}PIPERIDINE

Authors :   R. Xu, K. Aertgeerts

Date :   21 Nov 16 (Deposition) - 22 Feb 17 (Release) - 22 Mar 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.36

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

Reference :   L. Gomez, M. E. Massari, T. Vickers, G. Freestone, W. Vernier, K. Ly, R. Xu, M. Mccarrick, T. Marrone, M. Metz, Y. G. Yan, Z. W. Yoder, R. Lemus N. J. Broadbent, R. Barido, N. Warren, K. Schmelzer, D. Neul, D. Lee, C. B. Andersen, K. Sebring, K. Aertgeerts, X. Zhou, A. Tabatabaei, M. Peters, J. G. Breitenbucher
Design And Synthesis Of Novel And Selective Phosphodiesterase 2 (Pde2A) Inhibitors For The Treatment Of Memory Disorders.
J. Med. Chem. V. 60 2037 2017
PubMed-ID: 28165743 | Reference-DOI: 10.1021/ACS.JMEDCHEM.6B01793

Molecule 1 - CGMP-DEPENDENT 3',5'-CYCLIC PHOSPHODIESTERASE
	Chains	:	A, B, C, D
	EC Number	:	3.1.4.17
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Strain	:	BACULOVIRUS INSECT CELL HI5
	Expression System Taxid	:	7111
	Expression System Vector Type	:	BACMID
	Fragment	:	CATALYTIC DOMAIN, 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 (3, 12)

No.	Name	Count	Type	Full Name
1	7OJ	4	Ligand/Ion	(3-BROMO-4-FLUOROPHENYL)[(5S)-3,3-DIFLUORO-5-(5-METHYL[1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7-YL)PIPERIDIN-1-YL]METHANONE
2	MG	4	Ligand/Ion	MAGNESIUM ION
3	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	7OJ	1	Ligand/Ion	(3-BROMO-4-FLUOROPHENYL)[(5S)-3,3-DIFLUORO-5-(5-METHYL[1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7-YL)PIPERIDIN-1-YL]METHANONE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	7OJ	1	Ligand/Ion	(3-BROMO-4-FLUOROPHENYL)[(5S)-3,3-DIFLUORO-5-(5-METHYL[1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7-YL)PIPERIDIN-1-YL]METHANONE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	7OJ	1	Ligand/Ion	(3-BROMO-4-FLUOROPHENYL)[(5S)-3,3-DIFLUORO-5-(5-METHYL[1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7-YL)PIPERIDIN-1-YL]METHANONE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	7OJ	1	Ligand/Ion	(3-BROMO-4-FLUOROPHENYL)[(5S)-3,3-DIFLUORO-5-(5-METHYL[1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7-YL)PIPERIDIN-1-YL]METHANONE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR A:655 , HIS A:656 , LEU A:770 , GLN A:812 , ILE A:826 , TYR A:827 , PHE A:830 , MET A:847 , GLN A:859 , PHE A:862	binding site for residue 7OJ A 1001
02	AC2	SOFTWARE	HIS A:660 , HIS A:696 , ASP A:697 , ASP A:808 , HOH A:1122 , HOH A:1128	binding site for residue ZN A 1002
03	AC3	SOFTWARE	ASP A:697 , HOH A:1112 , HOH A:1115 , HOH A:1122 , HOH A:1129 , HOH A:1132	binding site for residue MG A 1003
04	AC4	SOFTWARE	TYR B:655 , HIS B:656 , LEU B:809 , GLN B:812 , ILE B:826 , TYR B:827 , PHE B:830 , MET B:847 , GLN B:859 , PHE B:862 , HOH B:1122	binding site for residue 7OJ B 1001
05	AC5	SOFTWARE	HIS B:660 , HIS B:696 , ASP B:697 , ASP B:808 , HOH B:1102 , HOH B:1135	binding site for residue ZN B 1002
06	AC6	SOFTWARE	ASP B:697 , HOH B:1102 , HOH B:1103 , HOH B:1105 , HOH B:1122 , HOH B:1130	binding site for residue MG B 1003
07	AC7	SOFTWARE	TYR C:655 , HIS C:656 , LEU C:770 , LEU C:809 , GLN C:812 , ILE C:826 , TYR C:827 , PHE C:830 , MET C:847 , GLN C:859 , PHE C:862 , HOH C:1117	binding site for residue 7OJ C 1001
08	AC8	SOFTWARE	HIS C:660 , HIS C:696 , ASP C:697 , ASP C:808 , MG C:1003 , HOH C:1102 , HOH C:1117	binding site for residue ZN C 1002
09	AC9	SOFTWARE	ASP C:697 , ZN C:1002 , HOH C:1101 , HOH C:1102 , HOH C:1108 , HOH C:1120 , HOH C:1128	binding site for residue MG C 1003
10	AD1	SOFTWARE	TYR D:655 , HIS D:656 , LEU D:770 , GLN D:812 , ILE D:826 , TYR D:827 , PHE D:830 , MET D:847 , GLN D:859 , PHE D:862 , HOH D:1114	binding site for residue 7OJ D 1001
11	AD2	SOFTWARE	HIS D:660 , HIS D:696 , ASP D:697 , ASP D:808 , MG D:1003 , HOH D:1110 , HOH D:1114	binding site for residue ZN D 1002
12	AD3	SOFTWARE	ASP D:697 , ZN D:1002 , HOH D:1102 , HOH D:1110 , HOH D:1111 , HOH D:1112 , HOH D:1130	binding site for residue MG D 1003

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

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

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

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

(no "Exon" information available for 5TZC)

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:343
                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tzc A 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 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..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhh....hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tzc 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:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh....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
                 5tzc C 578 MDDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLD 917
                                   587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907       917

Chain D from PDB  Type:PROTEIN  Length:336
                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhh...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
                 5tzc D 582 YTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLD 917
                                   591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911

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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 5TZC)

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

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

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	Ligands, Modified Residues, Ions
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	5tzc
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Ligands, Modified Residues, Ions (3, 12)

Sites (12, 12)

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