SMTL ID : 4bbg.1

Crystal structure of human kinesin Eg5 in complex with 3-(((2-Aminoethyl)sulfanyl)(3-ethylphenyl) phenylmethyl)phenol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.75 Å

Oligo State

homo-trimer

Ligands

3 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 13 residues within 4Å: Chain A: R.24, R.26, P.27, Q.106, T.107, G.108, T.109, G.110, K.111, T.112, F.113, E.118 Ligands: MG.2 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:R.24, A:G.108, A:T.109, A:G.110, A:K.111, A:T.112, A:T.112, A:F.113, A:E.118 Water bridges: A:R.24, A:K.111, A:T.112, A:T.112, A:T.112 Salt bridges: A:K.111 pi-Stacking: A:F.113, A:F.113 ADP.9: 13 residues within 4Å: Chain B: R.24, R.26, P.27, Q.106, T.107, G.108, T.109, G.110, K.111, T.112, F.113, E.118 Ligands: MG.10 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:R.24, B:G.108, B:T.109, B:T.109, B:G.110, B:K.111, B:T.112, B:F.113, B:E.118 Water bridges: B:R.24, B:K.111, B:T.112, B:T.112, B:T.112, B:T.112, B:T.112 Salt bridges: B:K.111 pi-Stacking: B:F.113, B:F.113 ADP.17: 13 residues within 4Å: Chain C: R.24, R.26, P.27, Q.106, T.107, G.108, T.109, G.110, K.111, T.112, F.113, E.118 Ligands: MG.18 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:R.24, C:G.108, C:T.109, C:T.109, C:G.110, C:K.111, C:T.112, C:F.113, C:E.118 Water bridges: C:R.24, C:K.111, C:T.112, C:T.112, C:T.112, C:T.112, C:T.112 Salt bridges: C:K.111 pi-Stacking: C:F.113, C:F.113

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: T.112 Ligands: ADP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.112, H2O.2, H2O.2, H2O.2, H2O.4 MG.10: 2 residues within 4Å: Chain B: T.112 Ligands: ADP.9 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.112, H2O.5, H2O.5, H2O.5, H2O.8 MG.18: 2 residues within 4Å: Chain C: T.112 Ligands: ADP.17 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:T.112, H2O.9, H2O.9, H2O.9, H2O.11

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

CL.3: 2 residues within 4Å: Chain A: C.43, A.74 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: I.79, P.131, R.138 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: F.185, D.186, R.318 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain A: L.30 Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: R.297 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: C.43, A.74 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: I.79, P.131, R.138 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: F.185, D.186, R.318 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain B: L.30 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain B: R.297 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain C: C.43, A.74 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain C: I.79, P.131, R.138 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain C: F.185, D.186, R.318 Ligand excluded by PLIP CL.23: 1 residues within 4Å: Chain C: L.30 Ligand excluded by PLIP CL.24: 1 residues within 4Å: Chain C: R.297 Ligand excluded by PLIP

3 x V02: 3-[(R)-2-azanylethylsulfanyl-(3-ethylphenyl)-phenyl-methyl]phenol(Non-covalent)

V02.6: 14 residues within 4Å: Chain A: T.112, E.116, G.117, E.118, R.119, D.130, L.132, A.133, P.137, Y.211, L.214, E.215, A.218, R.221 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.116, A:E.116, A:R.119, A:A.133, A:P.137, A:L.214 Hydrogen bonds: A:G.117, A:E.118 V02.14: 14 residues within 4Å: Chain B: T.112, E.116, G.117, E.118, R.119, D.130, L.132, A.133, P.137, Y.211, L.214, E.215, A.218, R.221 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:E.116, B:E.116, B:R.119, B:A.133, B:P.137, B:L.214 Hydrogen bonds: B:G.117, B:E.118 V02.22: 14 residues within 4Å: Chain C: T.112, E.116, G.117, E.118, R.119, D.130, L.132, A.133, P.137, Y.211, L.214, E.215, A.218, R.221 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:E.116, C:E.116, C:R.119, C:A.133, C:P.137, C:L.214 Hydrogen bonds: C:G.117, C:E.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Good, J.A.D. et al., Optimized S-Trityl-L-Cysteine-Based Inhibitors of Kinesin Spindle Protein with Potent in Vivo Antitumor Activity in Lung Cancer Xenograft Models. J.Med.Chem. (2013)

Release Date

2013-05-15

Peptides

KINESIN-LIKE PROTEIN KIF11: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

KINESIN-LIKE PROTEIN KIF11

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