SMTL ID : 4a9u.1

CRYSTAL STRUCTURE OF HUMAN CHK2 IN COMPLEX WITH BENZIMIDAZOLE CARBOXAMIDE INHIBITOR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.48 Å

Oligo State

homo-dimer

Ligands

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.1: 5 residues within 4Å: Chain A: L.173, G.201, Y.202, N.203, R.204 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.203, A:N.203, A:R.204, A:R.204, A:R.204 Water bridges: A:G.201 NO3.13: 5 residues within 4Å: Chain B: L.173, G.201, Y.202, N.203, R.204 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.203, B:N.203, B:R.204, B:R.204, B:R.204 Water bridges: B:G.201

18 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 5 residues within 4Å: Chain A: L.75, K.76, L.78, K.85, I.86 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: K.76, I.86, K.87, N.88, F.89 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: K.263, F.273, E.277, R.280, H.281, P.282 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: E.17, N.88, F.89, F.90 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: R.144, V.206 Chain B: V.193 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain A: E.277, R.280 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: Q.134, E.276, L.279, R.280 Ligand excluded by PLIP EDO.10: 2 residues within 4Å: Chain A: R.38, K.39 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: E.227, S.233, L.234, K.235 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain B: L.75, K.76, L.78, K.85, I.86 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain B: K.76, I.86, K.87, N.88, F.89 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain B: K.263, F.273, E.277, R.280, H.281, P.282 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain B: E.17, N.88, F.89, F.90 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain A: V.193 Chain B: R.144, V.206 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain B: E.277, R.280 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain B: Q.134, E.276, L.279, R.280 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain B: R.38, K.39 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain B: E.227, S.233, L.234, K.235 Ligand excluded by PLIP

2 x A9U: 2-{4-[(1-BENZYLPIPERIDIN-4-YL)METHOXY]PHENYL}-1H-BENZIMIDAZOLE-6-CARBOXAMIDE(Non-covalent)

A9U.3: 12 residues within 4Å: Chain A: L.24, V.32, K.47, L.99, M.102, E.103, G.105, E.106, L.152, Q.156, T.165, D.166 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.24, A:L.24, A:V.32, A:L.99, A:L.152, A:T.165 Hydrogen bonds: A:K.47, A:E.106, A:E.106, A:D.166 Water bridges: A:F.167 A9U.15: 12 residues within 4Å: Chain B: L.24, V.32, K.47, L.99, M.102, E.103, G.105, E.106, L.152, Q.156, T.165, D.166 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.24, B:L.24, B:V.32, B:L.99, B:L.152, B:T.165 Hydrogen bonds: B:K.47, B:E.106, B:D.166, B:D.166 Water bridges: B:F.167

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 2 residues within 4Å: Chain A: V.9, Y.10 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain B: V.9, Y.10 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Matijssen, C. et al., Benzimidazole Inhibitors of the Protein Kinase Chk2: Clarification of the Binding Mode by Flexible Side Chain Docking and Protein-Ligand Crystallography. Bioorg.Med.Chem. (2012)

Release Date

2012-10-10

Peptides

SERINE/THREONINE-PROTEIN KINASE CHK2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

SERINE/THREONINE-PROTEIN KINASE CHK2

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