Structure of PDB 3dz2 Chain B Binding Site BS01

Receptor Information

>3dz2 Chain B (length=60) Species: 9606 (Homo sapiens)

AHFFEGTEKLLEVWFSRQQQGSGDLRTIPRSEWDILLKDVQCSIISVTKT
DKQEAYVLSE

Ligand information

• Ligand ID: A8M
• InChI: InChI=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
• InChIKey: PCQBSZQRAFEGGW-SDBHATRESA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: Cc1nc2c(ncnc2n1C3C(C(C(O3)CN(C)CCCN)O)O)N
  OpenEye OEToolkits 1.5.0: Cc1nc2c(ncnc2n1[C@H]3[C@@H]([C@@H]([C@H](O3)C[N@@](C)CCCN)O)O)N
  CACTVS 3.341: CN(CCCN)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2c(C)nc3c(N)ncnc23
  ACDLabs 10.04: n2c1c(ncnc1n(c2C)C3OC(C(O)C3O)CN(CCCN)C)N
  CACTVS 3.341: CN(CCCN)C[CH]1O[CH]([CH](O)[CH]1O)n2c(C)nc3c(N)ncnc23
• Formula: C15 H25 N7 O3
• Name: 5'-[(3-aminopropyl)(methyl)amino]-5'-deoxy-8-methyladenosine
• ChEMBL: CHEMBL1187706
• ZINC: ZINC000040913762
• PDB chain: 3dz2 Chain A Residue 368

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3dz2 New Insights into the Design of Inhibitors of Human S-Adenosylmethionine Decarboxylase: Studies of Adenine C8 Substitution in Structural Analogues of S-Adenosylmethionine
• Resolution: 1.86 Å
• Binding residue (original residue number in PDB): F7 E11 S66 E67
• Binding residue (residue number reindexed from 1): F4 E8 S59 E60
• Annotation score: 2
• Binding affinity: PDBbind-CN: -logKd/Ki=4.15,IC50=70uM
  BindingDB: IC50=70000nM

Enzymatic activity

• Catalytic site (original residue number in PDB): E67
• Catalytic site (residue number reindexed from 1): E60
• Enzyme Commision number: 4.1.1.50: adenosylmethionine decarboxylase.

Gene Ontology

Molecular Function

• GO:0004014 adenosylmethionine decarboxylase activity

Biological Process

• GO:0008295 spermidine biosynthetic process

External links

• PDB: RCSB:3dz2, PDBe:3dz2, PDBj:3dz2
• PDBsum: 3dz2
• PubMed: 19209891
• UniProt: P17707|DCAM_HUMAN S-adenosylmethionine decarboxylase proenzyme (Gene Name=AMD1)