SMTL ID : 4c9x.1

Crystal structure of NUDT1 (MTH1) with S-crizotinib

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-dimer

Ligands

2 x VHS: 3-[(1S)-1-(2,6-DICHLORO-3-FLUOROPHENYL)ETHOXY]-5-(1-PIPERIDIN-4-YLPYRAZOL-4-YL)PYRIDIN-2-AMINE(Non-covalent)

VHS.1: 14 residues within 4Å: Chain A: Y.9, L.11, F.29, N.35, F.74, F.76, E.79, M.83, V.85, W.119, D.121, D.122, F.141 Ligands: CL.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.9, A:L.11, A:F.29, A:N.35, A:F.76, A:F.76, A:W.119 Hydrogen bonds: A:D.121 pi-Stacking: A:W.119, A:W.119 VHS.8: 14 residues within 4Å: Chain B: Y.9, L.11, F.29, N.35, F.74, F.76, E.79, M.83, V.85, W.119, D.121, D.122, F.141 Ligands: CL.9 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.9, B:L.11, B:F.29, B:N.35, B:F.76, B:F.76, B:W.119 Hydrogen bonds: B:D.121 pi-Stacking: B:W.119, B:W.119

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

CL.2: 5 residues within 4Å: Chain A: L.11, N.35, G.36, D.122 Ligands: VHS.1 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain B: L.11, N.35, G.36, D.122 Ligands: VHS.8 Ligand excluded by PLIP

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

SO4.3: 2 residues within 4Å: Chain A: H.136, R.153 4 PLIP interactions: 4 interactions with chain A Water bridges: A:G.137, A:R.153 Salt bridges: A:H.136, A:R.153 SO4.4: 4 residues within 4Å: Chain A: H.67, T.90, D.91, S.92 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.90, A:D.91, A:D.91, A:S.92 Salt bridges: A:H.67 SO4.5: 7 residues within 4Å: Chain A: K.140, L.148, D.149 Chain B: K.140, L.148, D.149 Ligands: SO4.12 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.149 Water bridges: A:K.140 Salt bridges: A:K.140, B:K.140 SO4.6: 3 residues within 4Å: Chain A: L.66, H.67, K.68 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.68 Water bridges: A:K.68, A:K.134, A:K.134 Salt bridges: A:H.67, A:K.68 SO4.7: 2 residues within 4Å: Chain A: T.96, P.97 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.96 SO4.10: 2 residues within 4Å: Chain B: H.136, R.153 4 PLIP interactions: 4 interactions with chain B Water bridges: B:G.137, B:R.153 Salt bridges: B:H.136, B:R.153 SO4.11: 4 residues within 4Å: Chain B: H.67, T.90, D.91, S.92 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.91, B:D.91, B:S.92 Salt bridges: B:H.67 SO4.12: 7 residues within 4Å: Chain A: K.140, L.148, D.149 Chain B: K.140, L.148, D.149 Ligands: SO4.5 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.149 Water bridges: B:K.140 Salt bridges: B:K.140, A:K.140 SO4.13: 3 residues within 4Å: Chain B: L.66, H.67, K.68 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.68 Water bridges: B:K.68, B:K.134, B:K.134 Salt bridges: B:H.67, B:K.68 SO4.14: 2 residues within 4Å: Chain B: T.96, P.97 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huber, K.V.M. et al., Stereospecific Targeting of Mth1 by (S)-Crizotinib as an Anticancer Strategy. Nature (2014)

Release Date

2014-04-02

Peptides

7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

7,8-DIHYDRO-8-OXOGUANINE TRIPHOSPHATASE

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