Structure of PDB 3hnb Chain M Binding Site BS01

Receptor Information

>3hnb Chain M (length=156) Species: 9606 (Homo sapiens)

SCSMPLGMESKAISDAQITASSYFTNMFATWSPSKARLHLQGRSNAWRPQ
VNNPKEWLQVDFQKTMKVTGVTTQGVKSLLTSMYVKEFLISSSQDGHQWT
LFFQNGKVKVFQGNQDSFTPVVNSLDPPLLTRYLRIHPQSWVHQIALRME
VLGCEA

Ligand information

• Ligand ID: 768
• InChI: InChI=1S/C23H28Cl2N4O2/c24-17-8-9-22(19(25)14-17)31-16-18(30)15-29-21-7-3-2-6-20(21)28(23(29)26)13-12-27-10-4-1-5-11-27/h2-3,6-9,14,18,26,30H,1,4-5,10-13,15-16H2/b26-23+/t18-/m1/s1
• InChIKey: QMRFKZWWZBZQKJ-MVXIZWJUSA-N
• SMILES:
  CACTVS 3.341: O[C@@H](COc1ccc(Cl)cc1Cl)CN2C(=N)N(CCN3CCCCC3)c4ccccc24
  OpenEye OEToolkits 1.5.0: [H]N=C1N(c2ccccc2N1CC(COc3ccc(cc3Cl)Cl)O)CCN4CCCCC4
  CACTVS 3.341: O[CH](COc1ccc(Cl)cc1Cl)CN2C(=N)N(CCN3CCCCC3)c4ccccc24
  ACDLabs 10.04: Clc4ccc(OCC(O)CN1c3ccccc3N(C1=[N@H])CCN2CCCCC2)c(Cl)c4
  OpenEye OEToolkits 1.5.0: [H]/N=C/1\N(c2ccccc2N1C[C@H](COc3ccc(cc3Cl)Cl)O)CCN4CCCCC4
• Formula: C23 H28 Cl2 N4 O2
• Name: (2R)-1-(2,4-dichlorophenoxy)-3-[(2E)-2-imino-3-(2-piperidin-1-ylethyl)-2,3-dihydro-1H-benzimidazol-1-yl]propan-2-ol;
  1-(2,4-dichlorophenoxy)-3-{2-imino-3-[2-(1-piperidinyl)ethyl]-2,3-dihydro-1H-benzimidazol-1-yl}-2-propanol
• PDB chain: 3hnb Chain M Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3hnb Trp2313-His2315 of factor VIII C2 domain is involved in membrane binding: structure of a complex between the C2 domain and an inhibitor of membrane binding.
• Resolution: 1.15 Å
• Binding residue (original residue number in PDB): K2258 Q2311 S2312 W2313 H2315
• Binding residue (residue number reindexed from 1): K86 Q139 S140 W141 H143
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=5.11,IC50=7.8uM
  BindingDB: IC50=7800nM

External links

• PDB: RCSB:3hnb, PDBe:3hnb, PDBj:3hnb
• PDBsum: 3hnb
• PubMed: 20089867
• UniProt: P00451|FA8_HUMAN Coagulation factor VIII (Gene Name=F8)