5TZ3 - JenaLib

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Title :   CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 2A IN COMPLEX WITH [1,2, 4]TRIAZOLO[1,5-A]PYRIMIDIN-7-YL}-N-(NAPHTHALENE-2-YL)PIPERIDINE-3-CARBOXAMIDE

Authors :   R. Xu, K. Aertgeerts

Date :   21 Nov 16 (Deposition) - 22 Feb 17 (Release) - 29 Mar 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.72

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	:	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	7OM	4	Ligand/Ion	(3~{R})-1-(5-METHYL-[1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7-YL)-~{N}-NAPHTHALEN-2-YL-PIPERIDINE-3-CARBOXAMIDE
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	7OM	1	Ligand/Ion	(3~{R})-1-(5-METHYL-[1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7-YL)-~{N}-NAPHTHALEN-2-YL-PIPERIDINE-3-CARBOXAMIDE
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	7OM	1	Ligand/Ion	(3~{R})-1-(5-METHYL-[1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7-YL)-~{N}-NAPHTHALEN-2-YL-PIPERIDINE-3-CARBOXAMIDE
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	7OM	1	Ligand/Ion	(3~{R})-1-(5-METHYL-[1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7-YL)-~{N}-NAPHTHALEN-2-YL-PIPERIDINE-3-CARBOXAMIDE
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	7OM	1	Ligand/Ion	(3~{R})-1-(5-METHYL-[1,2,4]TRIAZOLO[1,5-A]PYRIMIDIN-7-YL)-~{N}-NAPHTHALEN-2-YL-PIPERIDINE-3-CARBOXAMIDE
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 , LEU A:770 , GLN A:812 , ILE A:826 , PHE A:830 , MET A:847 , LEU A:858 , GLN A:859 , PHE A:862 , ILE A:866 , HOH A:1285	binding site for residue 7OM A 1001
02	AC2	SOFTWARE	HIS A:660 , HIS A:696 , ASP A:697 , ASP A:808 , MG A:1003 , HOH A:1139 , HOH A:1203	binding site for residue ZN A 1002
03	AC3	SOFTWARE	ASP A:697 , ZN A:1002 , HOH A:1135 , HOH A:1139 , HOH A:1177 , HOH A:1182 , HOH A:1221	binding site for residue MG A 1003
04	AC4	SOFTWARE	TYR B:655 , LEU B:770 , GLN B:812 , ILE B:826 , PHE B:830 , MET B:847 , LEU B:858 , GLN B:859 , SER B:861 , PHE B:862 , HOH B:1280	binding site for residue 7OM B 1001
05	AC5	SOFTWARE	HIS B:660 , HIS B:696 , ASP B:697 , ASP B:808 , MG B:1003 , HOH B:1121 , HOH B:1190	binding site for residue ZN B 1002
06	AC6	SOFTWARE	ASP B:697 , ZN B:1002 , HOH B:1121 , HOH B:1127 , HOH B:1129 , HOH B:1175 , HOH B:1220	binding site for residue MG B 1003
07	AC7	SOFTWARE	TYR C:655 , LEU C:809 , GLN C:812 , ILE C:826 , PHE C:830 , MET C:847 , LEU C:858 , GLN C:859 , SER C:861 , PHE C:862 , ILE C:866 , HOH C:1227	binding site for residue 7OM C 1001
08	AC8	SOFTWARE	HIS C:660 , HIS C:696 , ASP C:697 , ASP C:808 , HOH C:1114 , HOH C:1139	binding site for residue ZN C 1002
09	AC9	SOFTWARE	ASP C:697 , HOH C:1114 , HOH C:1121 , HOH C:1176 , HOH C:1187 , HOH C:1211	binding site for residue MG C 1003
10	AD1	SOFTWARE	TYR D:655 , LEU D:770 , LEU D:809 , GLN D:812 , ILE D:826 , PHE D:830 , MET D:847 , LEU D:858 , GLN D:859 , PHE D:862	binding site for residue 7OM D 1001
11	AD2	SOFTWARE	HIS D:660 , HIS D:696 , ASP D:697 , ASP D:808 , MG D:1003 , HOH D:1122 , HOH D:1168	binding site for residue ZN D 1002
12	AD3	SOFTWARE	ASP D:697 , ZN D:1002 , HOH D:1151 , HOH D:1168 , HOH D:1194 , HOH D:1213 , HOH D:1234	binding site for residue MG D 1003

(no "SS Bond" information available for 5TZ3)

(no "Cis Peptide Bond" information available for 5TZ3)

(no "SAP(SNP)/Variant" information available for 5TZ3)

(no "PROSITE Motif" information available for 5TZ3)

(no "Exon" information available for 5TZ3)

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:341
                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tz3 A 576 SAMDDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFL 916
                                   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: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
                 5tz3 B 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 C from PDB  Type:PROTEIN  Length:334
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tz3 C 580 DEYTKLGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFL 916
                                 ||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       862       872       882       892       902       912    
                               585|                                                                                                                                                                                                                                                                                                                                       
                                589

Chain D from PDB  Type:PROTEIN  Length:327
                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tz3 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 5TZ3)

(no "CATH Domain" information available for 5TZ3)

(no "Pfam Domain" information available for 5TZ3)

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	5tz3
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Description

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Ligands, Modified Residues, Ions (3, 12)

Sites (12, 12)

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