Structure of PDB 5c7d Chain A Binding Site BS02

Receptor Information

>5c7d Chain A (length=106) Species: 9606 (Homo sapiens)

NFPNSTNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKV
KCFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEQKGQEYINNIHLTHSL
EECLVR

Ligand information

• Ligand ID: 4YF
• InChI: InChI=1S/C14H19ClN4O/c1-10-8-18(5-3-16-10)9-14(20)19-4-2-11-7-17-13(15)6-12(11)19/h6-7,10,16H,2-5,8-9H2,1H3/p+1/t10-/m1/s1
• InChIKey: UIUNSWTUDREESN-SNVBAGLBSA-O
• SMILES:
  CACTVS 3.385: C[C@@H]1CN(CC[NH2+]1)CC(=O)N2CCc3cnc(Cl)cc23
  ACDLabs 12.01: CC1[NH2+]CCN(C1)CC(=O)N3CCc2c3cc(Cl)nc2
  OpenEye OEToolkits 1.9.2: CC1CN(CC[NH2+]1)CC(=O)N2CCc3c2cc(nc3)Cl
  OpenEye OEToolkits 1.9.2: C[C@@H]1CN(CC[NH2+]1)CC(=O)N2CCc3c2cc(nc3)Cl
  CACTVS 3.385: C[CH]1CN(CC[NH2+]1)CC(=O)N2CCc3cnc(Cl)cc23
• Formula: C14 H20 Cl N4 O
• Name: (2R)-4-[2-(6-chloro-2,3-dihydro-1H-pyrrolo[3,2-c]pyridin-1-yl)-2-oxoethyl]-2-methylpiperazin-1-ium
• PDB chain: 5c7d Chain A Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5c7d Fragment-Based Drug Discovery Targeting Inhibitor of Apoptosis Proteins: Discovery of a Non-Alanine Lead Series with Dual Activity Against cIAP1 and XIAP.
• Resolution: 2.25 Å
• Binding residue (original residue number in PDB): K297 G306 L307 T308 D309 W310 E314 Q319 W323 Y324
• Binding residue (residue number reindexed from 1): K49 G58 L59 T60 D61 W62 E66 Q71 W75 Y76
• Annotation score: 1
• Binding affinity: MOAD: ic50=7.7uM
  PDBbind-CN: -logKd/Ki=5.11,IC50=7.7uM

Enzymatic activity

• Enzyme Commision number: 2.3.2.27: RING-type E3 ubiquitin transferase.

External links

• PDB: RCSB:5c7d, PDBe:5c7d, PDBj:5c7d
• PDBsum: 5c7d
• PubMed: 26218264
• UniProt: P98170|XIAP_HUMAN E3 ubiquitin-protein ligase XIAP (Gene Name=XIAP)