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Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5XKM

Crystal structure of human phosphodiesterase 2A in complex with 6-methyl-N-(1-(4-(trifluoromethoxy)phenyl)propyl)pyrazolo[1,5-a]pyrimidine-3-carboxamide

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
A	0007165	biological_process	signal transduction
A	0008081	molecular_function	phosphoric diester hydrolase activity
B	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
B	0007165	biological_process	signal transduction
B	0008081	molecular_function	phosphoric diester hydrolase activity
C	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
C	0007165	biological_process	signal transduction
C	0008081	molecular_function	phosphoric diester hydrolase activity
D	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
D	0007165	biological_process	signal transduction
D	0008081	molecular_function	phosphoric diester hydrolase activity
E	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
E	0007165	biological_process	signal transduction
E	0008081	molecular_function	phosphoric diester hydrolase activity
F	0004114	molecular_function	3',5'-cyclic-nucleotide phosphodiesterase activity
F	0007165	biological_process	signal transduction
F	0008081	molecular_function	phosphoric diester hydrolase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	binding site for residue MG A 2001

Chain	Residue
A	ASP697
A	HOH2105
A	HOH2116
A	HOH2124
A	HOH2143
A	HOH2167

site_id	AC2
Number of Residues	6
Details	binding site for residue ZN A 2002

Chain	Residue
A	ASP808
A	HOH2116
A	HOH2161
A	HIS660
A	HIS696
A	ASP697

site_id	AC3
Number of Residues	5
Details	binding site for residue MG A 2003

Chain	Residue
A	GLU785
A	HOH2154
A	HOH2190
A	HOH2196
A	HOH2213

site_id	AC4
Number of Residues	17
Details	binding site for residue 87R A 2004

Chain	Residue
A	HIS656
A	THR768
A	LEU770
A	HIS773
A	THR805
A	ASP808
A	LEU809
A	GLN812
A	ILE826
A	TYR827
A	PHE830
A	GLN859
A	PHE862
A	ILE866
A	ILE870
A	HOH2115
A	HOH2132

site_id	AC5
Number of Residues	6
Details	binding site for residue MG B 2001

Chain	Residue
B	ASP697
B	HOH2106
B	HOH2110
B	HOH2142
B	HOH2144
B	HOH2154

site_id	AC6
Number of Residues	6
Details	binding site for residue ZN B 2002

Chain	Residue
B	HIS660
B	HIS696
B	ASP697
B	ASP808
B	HOH2110
B	HOH2132

site_id	AC7
Number of Residues	15
Details	binding site for residue 87R B 2003

Chain	Residue
B	HIS656
B	THR768
B	LEU770
B	HIS773
B	THR805
B	ASP808
B	LEU809
B	ILE826
B	TYR827
B	PHE830
B	GLN859
B	PHE862
B	ILE866
B	HOH2153
B	HOH2164

site_id	AC8
Number of Residues	6
Details	binding site for residue MG C 2001

Chain	Residue
C	ASP697
C	HOH2103
C	HOH2114
C	HOH2136
C	HOH2137
C	HOH2149

site_id	AC9
Number of Residues	6
Details	binding site for residue ZN C 2002

Chain	Residue
C	HIS660
C	HIS696
C	ASP697
C	ASP808
C	HOH2114
C	HOH2119

site_id	AD1
Number of Residues	17
Details	binding site for residue 87R C 2003

Chain	Residue
C	HIS656
C	THR768
C	LEU770
C	HIS773
C	THR805
C	ASP808
C	LEU809
C	GLN812
C	ILE826
C	TYR827
C	PHE830
C	GLN859
C	PHE862
C	ILE866
C	ILE870
C	HOH2150
C	HOH2155

site_id	AD2
Number of Residues	6
Details	binding site for residue MG D 2001

Chain	Residue
D	ASP697
D	HOH2107
D	HOH2118
D	HOH2139
D	HOH2144
D	HOH2162

site_id	AD3
Number of Residues	6
Details	binding site for residue ZN D 2002

Chain	Residue
D	ASP808
D	HOH2118
D	HOH2157
D	HIS660
D	HIS696
D	ASP697

site_id	AD4
Number of Residues	4
Details	binding site for residue MG D 2003

Chain	Residue
D	GLU785
D	HOH2174
D	HOH2191
E	HOH2143

site_id	AD5
Number of Residues	17
Details	binding site for residue 87R D 2004

Chain	Residue
D	HIS656
D	THR768
D	LEU770
D	HIS773
D	THR805
D	ASP808
D	LEU809
D	GLN812
D	ILE826
D	TYR827
D	PHE830
D	LEU858
D	GLN859
D	PHE862
D	ILE866
D	HOH2120
D	HOH2143

site_id	AD6
Number of Residues	6
Details	binding site for residue MG E 2001

Chain	Residue
E	ASP697
E	HOH2102
E	HOH2103
E	HOH2114
E	HOH2144
E	HOH2172

site_id	AD7
Number of Residues	6
Details	binding site for residue ZN E 2002

Chain	Residue
E	HIS660
E	HIS696
E	ASP697
E	ASP808
E	HOH2102
E	HOH2135

site_id	AD8
Number of Residues	15
Details	binding site for residue 87R E 2003

Chain	Residue
E	HIS656
E	THR768
E	LEU770
E	HIS773
E	THR805
E	ASP808
E	LEU809
E	GLN812
E	ILE826
E	LEU858
E	GLN859
E	PHE862
E	ILE866
E	HOH2108
E	HOH2111

site_id	AD9
Number of Residues	6
Details	binding site for residue MG F 2001

Chain	Residue
F	ASP697
F	HOH4001
F	HOH4005
F	HOH4013
F	HOH4063
F	HOH4065

site_id	AE1
Number of Residues	6
Details	binding site for residue ZN F 2002

Chain	Residue
F	HIS660
F	HIS696
F	ASP697
F	ASP808
F	HOH4001
F	HOH4042

site_id	AE2
Number of Residues	16
Details	binding site for residue 87R F 2003

Chain	Residue
F	HIS656
F	THR768
F	LEU770
F	HIS773
F	THR805
F	ASP808
F	LEU809
F	ILE826
F	TYR827
F	LEU858
F	GLN859
F	PHE862
F	ILE866
F	ILE870
F	HOH4004
F	HOH4025

Functional Information from PROSITE/UniProt

site_id	PS00126
Number of Residues	12
Details	PDEASE_I_1 3'5'-cyclic nucleotide phosphodiesterase domain signature. HDLdHrGtnNsF

Chain	Residue	Details
A	HIS696-PHE707

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	Active site: {"description":"Proton donor","evidences":[{"source":"UniProtKB","id":"O76083","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	18
Details	Binding site: {"evidences":[{"source":"PubMed","id":"15938621","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19828435","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23899287","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1Z1L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3IBJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ITM","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ITU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4HTX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4HTZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4JIB","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"15938621","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19828435","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23899287","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1Z1L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ITM","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ITU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4HTX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4HTZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4JIB","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	648
Details	Domain: {"description":"PDEase","evidences":[{"source":"PROSITE-ProRule","id":"PRU01192","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

247947

PDB entries from 2026-01-21

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