Structure of PDB 6gjw Chain D Binding Site BS02

Receptor Information

>6gjw Chain D (length=78) Species: 9606 (Homo sapiens)

EEFVEEFNRLKTFANFPSGSPVSASTLARAGFLYTGEGDTVRCFSCHAAV
DRWQYGDSAVGRHRKVSPNCRFINGFYL

Ligand information

• Ligand ID: F2H
• InChI: InChI=1S/C35H26N4O15S4/c40-33(38-25-13-15-27(55(43,44)45)23-9-3-11-29(31(23)25)57(49,50)51)19-5-1-7-21(17-19)36-35(42)37-22-8-2-6-20(18-22)34(41)39-26-14-16-28(56(46,47)48)24-10-4-12-30(32(24)26)58(52,53)54/h1-18H,(H,38,40)(H,39,41)(H2,36,37,42)(H,43,44,45)(H,46,47,48)(H,49,50,51)(H,52,53,54)/p-4
• InChIKey: DKTDCAGZLFSGDS-UHFFFAOYSA-J
• SMILES:
  CACTVS 3.385: [O-][S](=O)(=O)c1ccc(NC(=O)c2cccc(NC(=O)Nc3cccc(c3)C(=O)Nc4ccc(c5cccc(c45)[S]([O-])(=O)=O)[S]([O-])(=O)=O)c2)c6c1cccc6[S]([O-])(=O)=O
  OpenEye OEToolkits 2.0.6: c1cc(cc(c1)NC(=O)Nc2cccc(c2)C(=O)Nc3ccc(c4c3c(ccc4)S(=O)(=O)[O-])S(=O)(=O)[O-])C(=O)Nc5ccc(c6c5c(ccc6)S(=O)(=O)[O-])S(=O)(=O)[O-]
• Formula: C35 H22 N4 O15 S4
• Name: 4-[[3-[[3-[(4,8-disulfonatonaphthalen-1-yl)carbamoyl]phenyl]carbamoylamino]phenyl]carbonylamino]naphthalene-1,5-disulfonate
• PDB chain: 6gjw Chain D Residue 102

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6gjw Structure-Activity Relationship of NF023 Derivatives Binding to XIAP-BIR1.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): R62 C66 H67 S87 P88 N89
• Binding residue (residue number reindexed from 1): R42 C46 H47 S67 P68 N69
• Annotation score: 1
• Binding affinity: MOAD: Kd=9uM
  PDBbind-CN: -logKd/Ki=4.96,Kd=11uM

Enzymatic activity

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

External links

• PDB: RCSB:6gjw, PDBe:6gjw, PDBj:6gjw
• PDBsum: 6gjw
• PubMed: 31011505
• UniProt: P98170|XIAP_HUMAN E3 ubiquitin-protein ligase XIAP (Gene Name=XIAP)