Structure of PDB 2w1d Chain A Binding Site BS01

Receptor Information

>2w1d Chain A (length=251) Species: 9606 (Homo sapiens)

QWALEDFEIGRPLGKGKFGNVYLAREKQSKFILALKVLFKAQLEKAGVEH
QLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQKLS
KFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSAGELKIADFG
WSVGTLDYLPPEMIEGRMHDKVDLWSLGVLCYEFLVGKPPFEANTYQETY
KRISRVEFTFPDFVTEGARDLISRLLKHNPSQRPMLREVLEHPWITANSS
K

Ligand information

• Ligand ID: L0D
• InChI: InChI=1S/C10H8N4/c1-2-4-8-7(3-1)12-10(13-8)9-5-6-11-14-9/h1-6H,(H,11,14)(H,12,13)
• InChIKey: IYTGPPNUOLLGBE-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04: n2c1c(cccc1)nc2c3nncc3
  CACTVS 3.341: [nH]1ccc(n1)c2[nH]c3ccccc3n2
  OpenEye OEToolkits 1.5.0: c1ccc2c(c1)[nH]c(n2)c3cc[nH]n3
• Formula: C10 H8 N4
• Name: 2-(1H-pyrazol-3-yl)-1H-benzimidazole
• ChEMBL: CHEMBL495758
• DrugBank: DB08065
• ZINC: ZINC000005687459
• PDB chain: 2w1d Chain A Residue 1391

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2w1d Fragment-Based Discovery of the Pyrazol-4-Yl Urea (at9283), a Multitargeted Kinase Inhibitor with Potent Aurora Kinase Activity.
• Resolution: 2.97 Å
• Binding residue (original residue number in PDB): A160 Y212 A213 G216 L263 K389
• Binding residue (residue number reindexed from 1): A34 Y86 A87 G90 L137 K251
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=6.04,IC50=0.91uM
  BindingDB: IC50=910nM

Enzymatic activity

• Catalytic site (original residue number in PDB): D256 K258 E260 N261 D274 T292
• Catalytic site (residue number reindexed from 1): D130 K132 E134 N135 D148 T155
• Enzyme Commision number: 2.7.11.1: non-specific serine/threonine protein kinase.

Gene Ontology

Molecular Function

• GO:0004672 protein kinase activity
• GO:0005524 ATP binding

Biological Process

• GO:0006468 protein phosphorylation

External links

• PDB: RCSB:2w1d, PDBe:2w1d, PDBj:2w1d
• PDBsum: 2w1d
• PubMed: 19143567
• UniProt: O14965|AURKA_HUMAN Aurora kinase A (Gene Name=AURKA)