SMTL ID : 3f5x.1 (3 other biounits)

CDK-2-Cyclin complex with indazole inhibitor 9 bound at its active site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-4-4-mer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 6 residues within 4Å: Chain A: F.4, N.23, E.28, L.67, D.68 Chain H: M.70 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain H Hydrogen bonds: A:N.23, A:E.28, A:D.68, A:D.68 Water bridges: A:E.28, H:S.71, H:S.71, H:S.71 GOL.4: 6 residues within 4Å: Chain C: F.4, N.23, E.28, L.67, D.68 Chain F: M.70 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain F Hydrogen bonds: C:N.23, C:D.68 Water bridges: C:E.28, F:S.71, F:S.71, F:S.71 GOL.7: 9 residues within 4Å: Chain D: S.69, M.70 Chain E: F.4, N.23, E.28, V.30, L.67, D.68, V.79 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:N.23, E:E.28, E:D.68, D:S.69 GOL.9: 9 residues within 4Å: Chain B: S.69, M.70 Chain G: F.4, N.23, E.28, V.30, L.67, D.68, V.79 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain B Hydrogen bonds: G:N.23, B:S.69 Water bridges: G:T.26

4 x EZV: 4-{3-[7-(4-methylpiperazin-1-yl)-1H-benzimidazol-2-yl]-1H-indazol-6-yl}aniline(Non-covalent)

EZV.2: 18 residues within 4Å: Chain A: I.10, A.31, K.33, E.51, L.55, V.64, F.80, E.81, F.82, L.83, H.84, D.86, K.89, Q.131, L.134, A.144, D.145, F.146 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:A.31, A:L.55, A:V.64, A:F.80, A:F.82, A:L.134, A:A.144 Hydrogen bonds: A:E.51, A:E.51, A:E.81, A:L.83, A:K.89, A:D.145, A:F.146 Salt bridges: A:D.86 pi-Stacking: A:F.80 EZV.5: 18 residues within 4Å: Chain C: I.10, A.31, K.33, E.51, L.55, V.64, F.80, E.81, F.82, L.83, H.84, D.86, K.89, Q.131, L.134, A.144, D.145, F.146 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:A.31, C:L.55, C:V.64, C:F.80, C:F.82, C:L.134, C:A.144 Hydrogen bonds: C:E.51, C:E.81, C:L.83, C:K.89, C:D.145, C:F.146 Salt bridges: C:D.86 pi-Stacking: C:F.80 EZV.8: 18 residues within 4Å: Chain E: I.10, A.31, K.33, E.51, L.55, V.64, F.80, E.81, F.82, L.83, H.84, D.86, K.89, Q.131, L.134, A.144, D.145, F.146 14 PLIP interactions: 14 interactions with chain E Hydrophobic interactions: E:L.55, E:V.64, E:F.80, E:F.82, E:L.134, E:A.144 Hydrogen bonds: E:E.51, E:E.51, E:E.81, E:L.83, E:D.145, E:F.146 Salt bridges: E:D.86 pi-Stacking: E:F.80 EZV.10: 18 residues within 4Å: Chain G: I.10, A.31, K.33, E.51, L.55, V.64, F.80, E.81, F.82, L.83, H.84, D.86, K.89, Q.131, L.134, A.144, D.145, F.146 13 PLIP interactions: 13 interactions with chain G Hydrophobic interactions: G:L.55, G:V.64, G:F.80, G:F.82, G:L.134, G:A.144 Hydrogen bonds: G:E.51, G:E.81, G:L.83, G:D.145, G:F.146 Salt bridges: G:D.86 pi-Stacking: G:F.80

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain B: R.234, K.238, L.247 3 PLIP interactions: 3 interactions with chain B Water bridges: B:E.235 Salt bridges: B:R.234, B:K.238 SO4.6: 3 residues within 4Å: Chain D: R.234, K.238, L.247 3 PLIP interactions: 3 interactions with chain D Water bridges: D:R.234 Salt bridges: D:R.234, D:K.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Trujillo, J.I. et al., 2-(6-Phenyl-1H-indazol-3-yl)-1H-benzo[d]imidazoles: Design and synthesis of a potent and isoform selective PKC-zeta inhibitor. Bioorg.Med.Chem.Lett. (2009)

Release Date

2009-02-03

Peptides

Cell division protein kinase 2: ACEG
Cyclin-A2: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
C

E
A

G
A

B
D

D
D

F
B

H
B

Cell division protein kinase 2

Cyclin-A2

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