Structure of PDB 4ibg Chain B Binding Site BS01

Receptor Information

>4ibg Chain B (length=123) Species: 128952 (Ebola virus - Mayinga, Zaire, 1976)

DISAKDLRNIMYDHLPGFGTAFHQLVQVICKLGKDSNSLDIIHAEFQASL
AEGDSPQCALIQITKRVPIFQDAAPPVIHIRSRGDIPRACQKSLRPVPPS
PKIDRGWVCVFQLQDGKTLGLKI

Ligand information

• Ligand ID: 1D6
• InChI: InChI=1S/C27H20ClNO7/c1-14-3-2-4-16(9-14)24(32)22-23(17-11-19(28)26-20(12-17)35-13-36-26)29(27(34)25(22)33)18-7-5-15(6-8-18)10-21(30)31/h2-9,11-12,23,33H,10,13H2,1H3,(H,30,31)/t23-/m0/s1
• InChIKey: UREMFAJAZZTMEH-QHCPKHFHSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: Cc1cccc(c1)C(=O)C2=C(C(=O)N(C2c3cc4c(c(c3)Cl)OCO4)c5ccc(cc5)CC(=O)O)O
  CACTVS 3.370: Cc1cccc(c1)C(=O)C2=C(O)C(=O)N([CH]2c3cc(Cl)c4OCOc4c3)c5ccc(CC(O)=O)cc5
  CACTVS 3.370: Cc1cccc(c1)C(=O)C2=C(O)C(=O)N([C@H]2c3cc(Cl)c4OCOc4c3)c5ccc(CC(O)=O)cc5
  ACDLabs 12.01: O=C(O)Cc1ccc(cc1)N5C(=O)C(O)=C(C(=O)c2cccc(c2)C)C5c3cc4OCOc4c(Cl)c3
  OpenEye OEToolkits 1.7.6: Cc1cccc(c1)C(=O)C2=C(C(=O)N([C@H]2c3cc4c(c(c3)Cl)OCO4)c5ccc(cc5)CC(=O)O)O
• Formula: C27 H20 Cl N O7
• Name: {4-[(2S)-2-(7-chloro-1,3-benzodioxol-5-yl)-4-hydroxy-3-(3-methylbenzoyl)-5-oxo-2,5-dihydro-1H-pyrrol-1-yl]phenyl}acetic acid
• ZINC: ZINC000098207948
• PDB chain: 4ibg Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4ibg In Silico Derived Small Molecules Bind the Filovirus VP35 Protein and Inhibit Its Polymerase Cofactor Activity.
• Resolution: 1.413 Å
• Binding residue (original residue number in PDB): Q241 V245 K248 K251 P293 I295
• Binding residue (residue number reindexed from 1): Q24 V28 K31 K34 P76 I78
• Annotation score: 1
• Binding affinity: MOAD: Kd=108uM
  PDBbind-CN: -logKd/Ki=3.97,Kd=108.0uM

External links

• PDB: RCSB:4ibg, PDBe:4ibg, PDBj:4ibg
• PDBsum: 4ibg
• PubMed: 24495995
• UniProt: Q05127|VP35_EBOZM Polymerase cofactor VP35 (Gene Name=VP35)