Structure of PDB 3dz6 Chain B Binding Site BS01

Receptor Information

>3dz6 Chain B (length=56) Species: 9606 (Homo sapiens)

HFFEGTEKLLEVWFSRGSGDLRTIPRSEWDILLKDVQCSIISVTKTDKQE
AYVLSE

Ligand information

• Ligand ID: M8E
• InChI: InChI=1S/C17H27N7O4/c1-3-11-22-12-15(18)20-9-21-16(12)24(11)17-14(26)13(25)10(28-17)8-23(2)6-4-5-7-27-19/h3,9-10,13-14,17,25-26H,1,4-8,19H2,2H3,(H2,18,20,21)/t10-,13-,14-,17-/m1/s1
• InChIKey: XUKYGMIDWKBMIW-IWCJZZDYSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CN(CCCCON)CC1C(C(C(O1)n2c(nc3c2ncnc3N)C=C)O)O
  OpenEye OEToolkits 1.5.0: C[N@@](CCCCON)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2c(nc3c2ncnc3N)C=C)O)O
  ACDLabs 10.04: n2c1c(ncnc1n(c2\C=C)C3OC(C(O)C3O)CN(CCCCON)C)N
  CACTVS 3.341: CN(CCCCON)C[CH]1O[CH]([CH](O)[CH]1O)n2c(C=C)nc3c(N)ncnc23
  CACTVS 3.341: CN(CCCCON)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2c(C=C)nc3c(N)ncnc23
• Formula: C17 H27 N7 O4
• Name: 5'-{[4-(aminooxy)butyl](methyl)amino}-5'-deoxy-8-ethenyladenosine
• DrugBank: DB08163
• ZINC: ZINC000053683388
• PDB chain: 3dz6 Chain A Residue 368

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3dz6 New Insights into the Design of Inhibitors of Human S-Adenosylmethionine Decarboxylase: Studies of Adenine C8 Substitution in Structural Analogues of S-Adenosylmethionine
• Resolution: 1.83 Å
• Binding residue (original residue number in PDB): F7 L65 S66 E67
• Binding residue (residue number reindexed from 1): F3 L54 S55 E56
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=7.82,IC50=15nM

Enzymatic activity

• Catalytic site (original residue number in PDB): E67
• Catalytic site (residue number reindexed from 1): E56
• 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:3dz6, PDBe:3dz6, PDBj:3dz6
• PDBsum: 3dz6
• PubMed: 19209891
• UniProt: P17707|DCAM_HUMAN S-adenosylmethionine decarboxylase proenzyme (Gene Name=AMD1)