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2HD1

Crystal structure of PDE9 in complex with IBMX

Replaces:  1TBM
Functional Information from GO Data
ChainGOidnamespacecontents
A0004114molecular_function3',5'-cyclic-nucleotide phosphodiesterase activity
A0007165biological_processsignal transduction
A0008081molecular_functionphosphoric diester hydrolase activity
B0004114molecular_function3',5'-cyclic-nucleotide phosphodiesterase activity
B0007165biological_processsignal transduction
B0008081molecular_functionphosphoric diester hydrolase activity
Functional Information from PDB Data
site_idAC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE ZN A 101
ChainResidue
AMG102
AHIS256
AHIS292
AASP293
AASP402
AHOH507

site_idAC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG A 102
ChainResidue
AHOH509
AHOH510
AHOH511
AZN101
AASP293
AHOH508

site_idAC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE ZN B 101
ChainResidue
BMG102
BHIS256
BHIS292
BASP293
BASP402

site_idAC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG B 102
ChainResidue
BZN101
BASP293
BHOH508
BHOH509
BHOH510
BHOH511

site_idAC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE IBM A 1
ChainResidue
AILE403
ALEU420
ATYR424
AGLN453
APHE456

site_idAC6
Number of Residues7
DetailsBINDING SITE FOR RESIDUE IBM B 1
ChainResidue
AALA499
BLEU420
BTYR424
BPHE441
BALA452
BGLN453
BPHE456

Functional Information from PROSITE/UniProt
site_idPS00126
Number of Residues12
DetailsPDEASE_I_1 3'5'-cyclic nucleotide phosphodiesterase domain signature. HDLdHpGynNtY
ChainResidueDetails
AHIS292-TYR303

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues2
DetailsActive site: {"description":"Proton donor","evidences":[{"source":"PubMed","id":"18757755","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues12
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"18757755","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues8
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"18757755","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19919087","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20121115","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21483814","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22985069","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23025719","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2HD1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2YY2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3DYN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3JSI","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3JSW","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3K3E","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3K3H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3N3Z","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4E90","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4G2J","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4G2L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4GH6","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"Q8QZV1","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails

238895

PDB entries from 2025-07-16

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