SMTL ID : 2xae.1

Crystal structure of human kinesin Eg5 in complex with (R)-2-amino-3-((S)-2-methyl-1,1-diphenylbutylthio)propanoic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-trimer

Ligands

3 x 2XA: (2R)-2-AMINO-3-[(4-CHLOROPHENYL)-DIPHENYL-METHYL]SULFANYL-PROPANOIC ACID(Non-covalent)

2XA.1: 14 residues within 4Å: Chain A: T.112, E.116, G.117, E.118, R.119, W.127, A.133, P.137, L.160, Y.211, L.214, E.215, A.218, R.221 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:E.116, A:E.116, A:R.119, A:A.133, A:P.137, A:P.137, A:Y.211, A:L.214, A:L.214, A:E.215, A:E.215 Hydrogen bonds: A:E.116, A:E.116, A:E.116 Salt bridges: A:R.221 2XA.5: 14 residues within 4Å: Chain B: T.112, E.116, G.117, E.118, R.119, W.127, A.133, I.136, P.137, L.160, Y.211, L.214, E.215, R.221 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:E.116, B:R.119, B:W.127, B:A.133, B:I.136, B:P.137, B:Y.211, B:L.214 Hydrogen bonds: B:E.116, B:G.117 Salt bridges: B:R.221 2XA.10: 12 residues within 4Å: Chain C: T.112, E.116, G.117, E.118, R.119, W.127, A.133, P.137, Y.211, L.214, E.215, R.221 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:E.116, C:R.119, C:A.133, C:P.137, C:Y.211, C:L.214, C:E.215 Hydrogen bonds: C:E.116, C:E.116, C:G.117, C:R.221 Water bridges: C:E.118

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.112, S.232 Ligands: ADP.3 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:T.112, H2O.2, H2O.2, H2O.5, H2O.5 MG.6: 2 residues within 4Å: Chain B: T.112 Ligands: ADP.7 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:T.112, H2O.7, H2O.10, H2O.11, H2O.11 MG.11: 2 residues within 4Å: Chain C: T.112 Ligands: ADP.12 No protein-ligand interaction detected (PLIP)

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

ADP.3: 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 18 PLIP interactions: 18 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:F.113, A:E.118 Water bridges: A:R.24, A:N.29, A:T.107, A:K.111, A:T.112, A:T.112, A:D.265 Salt bridges: A:K.111 pi-Stacking: A:F.113, A:F.113 ADP.7: 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.6 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:R.24, B:G.108, B:T.109, B:G.110, B:K.111, B:T.112, B:T.112, B:F.113, B:E.118 Water bridges: B:R.24, B:T.107, B:K.111, B:K.111, B:K.111 Salt bridges: B:K.111 pi-Stacking: B:F.113, B:F.113 ADP.12: 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.11 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:T.112, C:F.113, C:E.118 Water bridges: C:R.24, C:T.107, C:K.111, C:K.111, C:K.111, C:T.112 Salt bridges: C:K.111 pi-Stacking: C:F.113, C:F.113

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

CL.4: 2 residues within 4Å: Chain A: N.29, L.30 Ligand excluded by PLIP

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

SO4.8: 5 residues within 4Å: Chain B: M.184, F.185, D.186, R.312, R.318 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.186, B:D.186 Salt bridges: B:R.312, B:R.318 SO4.9: 5 residues within 4Å: Chain B: V.41, E.42, C.43, G.73, A.74 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.41, B:E.42, B:C.43, B:A.74 SO4.13: 5 residues within 4Å: Chain C: M.184, F.185, D.186, R.312, R.318 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.186, C:D.186 Salt bridges: C:R.312, C:R.318

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kaan, H.Y.K. et al., Structure-Activity Relationship and Multidrug Resistance Study of New S-Trityl-L-Cysteine Derivatives as Inhibitors of Eg5. J.Med.Chem. (2011)

Release Date

2011-03-30

Peptides

KINESIN-LIKE PROTEIN KIF11: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

KINESIN-LIKE PROTEIN KIF11

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