SMTL ID : 4bdi.1

Fragment-based screening identifies a new area for inhibitor binding to checkpoint kinase 2 (CHK2)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-dimer

Ligands

2 x HAU: 1-acetyl-N-(5-methylpyridin-2-yl)piperidine-4-carboxamide(Non-covalent)

HAU.1: 10 residues within 4Å: Chain A: L.24, V.32, A.45, L.99, E.100, L.101, M.102, E.103, G.105, L.152 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.24, A:V.32, A:A.45, A:L.99, A:L.152 Hydrogen bonds: A:M.102, A:M.102 HAU.11: 10 residues within 4Å: Chain B: L.24, V.32, A.45, L.99, E.100, L.101, M.102, E.103, G.105, L.152 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.24, B:V.32, B:A.45, B:L.99, B:L.152 Hydrogen bonds: B:M.102, B:M.102

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

NO3.2: 5 residues within 4Å: Chain A: L.173, G.201, Y.202, N.203, R.204 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.203, A:N.203, A:R.204, A:R.204, A:R.204 NO3.12: 5 residues within 4Å: Chain B: L.173, G.201, Y.202, N.203, R.204 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.203, B:N.203, B:R.204, B:R.204, B:R.204

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

CL.3: 3 residues within 4Å: Chain A: V.9, Y.10 Ligands: EDO.9 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: V.9, Y.10 Ligands: EDO.19 Ligand excluded by PLIP

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

EDO.4: 4 residues within 4Å: Chain A: A.251, E.252, V.253, S.254 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.252 EDO.5: 6 residues within 4Å: Chain A: K.263, F.273, E.277, R.280, H.281, P.282 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.263, A:K.263, A:E.277 Water bridges: A:R.280 EDO.6: 4 residues within 4Å: Chain A: N.203, V.206 Chain B: E.192, V.193 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.192 Water bridges: A:V.206 EDO.7: 6 residues within 4Å: Chain A: L.75, K.76, L.78, N.79, K.85, I.86 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.79, A:I.86, A:I.86 EDO.8: 2 residues within 4Å: Chain A: Q.134, E.138 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.138 EDO.9: 5 residues within 4Å: Chain A: M.7, S.8, Y.10 Ligands: CL.3, EDO.10 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.8 EDO.10: 2 residues within 4Å: Chain A: M.7 Ligands: EDO.9 No protein-ligand interaction detected (PLIP) EDO.14: 4 residues within 4Å: Chain B: A.251, E.252, V.253, S.254 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.252 EDO.15: 6 residues within 4Å: Chain B: K.263, F.273, E.277, R.280, H.281, P.282 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.263, B:K.263, B:E.277 Water bridges: B:R.280 EDO.16: 4 residues within 4Å: Chain A: E.192, V.193 Chain B: N.203, V.206 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.192 Water bridges: B:V.206 EDO.17: 6 residues within 4Å: Chain B: L.75, K.76, L.78, N.79, K.85, I.86 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.79, B:I.86, B:I.86 EDO.18: 2 residues within 4Å: Chain B: Q.134, E.138 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.138 EDO.19: 5 residues within 4Å: Chain B: M.7, S.8, Y.10 Ligands: CL.13, EDO.20 1 PLIP interactions: 1 interactions with chain B Water bridges: B:S.8 EDO.20: 2 residues within 4Å: Chain B: M.7 Ligands: EDO.19 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Silva-Santisteban, M.C. et al., Fragment-Based Screening Maps Inhibitor Interactions in the ATP-Binding Site of Checkpoint Kinase 2. Plos One (2013)

Release Date

2013-06-26

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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