Structure of PDB 3dz2 Chain A Binding Site BS01

Receptor Information
>3dz2 Chain A (length=246) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
cSMFVSKRRFILKTCGTTLLLKALVPLLKLARDYSGFDSIQSFFYSRKNF
MKPSHQGYPHRNFQEEIEFLNAIFPNGAAYCMGRMNSDCWYLYTLDFPES
QPDQTLEILMSELDPAVMDQFYMKDGVTAKDVTRESGIRDLIPGSVIDAT
MFNPCGYSMNGMKSDGTYWTIHITPEPEFSYVSFETNLSQTSYDDLIRKV
VEVFKPGKFVTTLFVNQSSKCEGFKRLDCQSAMFNDYNFVFTSFAK
Ligand information
Ligand IDA8M
InChIInChI=1S/C15H25N7O3/c1-8-20-10-13(17)18-7-19-14(10)22(8)15-12(24)11(23)9(25-15)6-21(2)5-3-4-16/h7,9,11-12,15,23-24H,3-6,16H2,1-2H3,(H2,17,18,19)/t9-,11-,12-,15-/m1/s1
InChIKeyPCQBSZQRAFEGGW-SDBHATRESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1nc2c(ncnc2n1C3C(C(C(O3)CN(C)CCCN)O)O)N
OpenEye OEToolkits 1.5.0Cc1nc2c(ncnc2n1[C@H]3[C@@H]([C@@H]([C@H](O3)C[N@@](C)CCCN)O)O)N
CACTVS 3.341CN(CCCN)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2c(C)nc3c(N)ncnc23
ACDLabs 10.04n2c1c(ncnc1n(c2C)C3OC(C(O)C3O)CN(CCCN)C)N
CACTVS 3.341CN(CCCN)C[CH]1O[CH]([CH](O)[CH]1O)n2c(C)nc3c(N)ncnc23
FormulaC15 H25 N7 O3
Name5'-[(3-aminopropyl)(methyl)amino]-5'-deoxy-8-methyladenosine
ChEMBLCHEMBL1187706
DrugBank
ZINCZINC000040913762
PDB chain3dz2 Chain A Residue 368 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3dz2 New Insights into the Design of Inhibitors of Human S-Adenosylmethionine Decarboxylase: Studies of Adenine C8 Substitution in Structural Analogues of S-Adenosylmethionine
Resolution1.86 Å
Binding residue
(original residue number in PDB)		X68 C82 F223 N224 C226 G227 Y228 H243 I244 T245 E247
Binding residue
(residue number reindexed from 1)		X1 C15 F152 N153 C155 G156 Y157 H172 I173 T174 E176
Annotation score2
Binding affinityMOAD: ic50=70uM
PDBbind-CN: -logKd/Ki=4.15,IC50=70uM
BindingDB: IC50=70000nM
Enzymatic activity
Catalytic site (original residue number in PDB) S229 H243
Catalytic site (residue number reindexed from 1) S157 H171
Enzyme Commision number 4.1.1.50: adenosylmethionine decarboxylase.
Gene Ontology
Molecular Function
GO:0004014 adenosylmethionine decarboxylase activity
Biological Process
GO:0006597 spermine biosynthetic process
GO:0008295 spermidine biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3dz2, PDBe:3dz2, PDBj:3dz2
PDBsum3dz2
PubMed19209891
UniProtP17707|DCAM_HUMAN S-adenosylmethionine decarboxylase proenzyme (Gene Name=AMD1)

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