Structure of PDB 4ncm Chain A Binding Site BS01

Receptor Information

>4ncm Chain A (length=163) Species: 392809 (Influenza A virus (A/Victoria/3/1975(H3N2)))

SSFSFGGFTFKRTSGSSIKREEEVLTGNLQTLKIRVHEGYEEFTMVGKRA
TAILRKATRRLVQLIVSGKDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNF
VNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEHIDNVMGMVGVLPDMTPS
TEMSMRGIRVSKM

Ligand information

• Ligand ID: 704
• InChI: InChI=1S/C16H16ClFN6O/c1-8(16(25)24(2)3)22-15-12(18)7-21-14(23-15)11-6-20-13-10(11)4-9(17)5-19-13/h4-8H,1-3H3,(H,19,20)(H,21,22,23)/t8-/m0/s1
• InChIKey: RYLYZVYXGULJRD-QMMMGPOBSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: CC(C(=O)N(C)C)Nc1c(cnc(n1)c2c[nH]c3c2cc(cn3)Cl)F
  ACDLabs 12.01: O=C(N(C)C)C(Nc1nc(ncc1F)c3c2cc(Cl)cnc2nc3)C
  OpenEye OEToolkits 1.7.6: C[C@@H](C(=O)N(C)C)Nc1c(cnc(n1)c2c[nH]c3c2cc(cn3)Cl)F
  CACTVS 3.385: C[C@H](Nc1nc(ncc1F)c2c[nH]c3ncc(Cl)cc23)C(=O)N(C)C
  CACTVS 3.385: C[CH](Nc1nc(ncc1F)c2c[nH]c3ncc(Cl)cc23)C(=O)N(C)C
• Formula: C16 H16 Cl F N6 O
• Name: N~2~-[2-(5-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-fluoropyrimidin-4-yl]-N,N-dimethyl-L-alaninamide
• ChEMBL: CHEMBL3317969
• ZINC: ZINC000098208558
• PDB chain: 4ncm Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4ncm Discovery of a Novel, First-in-Class, Orally Bioavailable Azaindole Inhibitor (VX-787) of Influenza PB2.
• Resolution: 2.82 Å
• Binding residue (original residue number in PDB): F323 F325 H357 E361 F404 M431
• Binding residue (residue number reindexed from 1): F3 F5 H37 E41 F84 M111
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=7.00,Kd=0.10uM

External links

• PDB: RCSB:4ncm, PDBe:4ncm, PDBj:4ncm
• PDBsum: 4ncm
• PubMed: 25019388
• UniProt: P31345|PB2_I75A3 Polymerase basic protein 2 (Gene Name=PB2)