SMTL ID : 6aa4.2 (1 other biounit)

Crystal structure of MTH1 in complex with alpha-mangostin (cocktail No. 9)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: L.5, D.81, H.83, H.158, H.160 Chain B: H.158 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.81, A:D.81, A:H.83, A:H.158, A:H.160 ZN.2: 4 residues within 4Å: Chain A: E.40, H.163 Chain B: H.161, H.162 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Metal complexes: B:H.161, B:H.162, A:E.40, A:E.40, A:H.163 ZN.5: 6 residues within 4Å: Chain A: H.158 Chain B: L.5, D.81, H.83, H.158, H.160 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.81, B:D.81, B:H.83, B:H.158, B:H.160 ZN.6: 4 residues within 4Å: Chain A: H.161, H.162 Chain B: E.40, H.163 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:E.40, B:E.40, B:H.163, A:H.161, A:H.162

2 x MKS: 1,3,6-trihydroxy-7-methoxy-2,8-bis(3-methylbut-2-en-1-yl)-9H-xanthen-9-one(Non-covalent)

MKS.3: 14 residues within 4Å: Chain A: Y.6, T.7, L.8, F.26, N.32, F.71, F.73, M.80, W.116, D.118, D.119, F.138, G.140, Q.141 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.6, A:F.26, A:F.71, A:W.116, A:W.116, A:F.138 Hydrogen bonds: A:N.32, A:D.118 pi-Stacking: A:W.116, A:W.116, A:W.116, A:F.138 MKS.7: 14 residues within 4Å: Chain B: Y.6, T.7, L.8, F.26, N.32, F.71, F.73, M.80, W.116, D.118, D.119, F.138, G.140, Q.141 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.6, B:F.26, B:F.71, B:W.116, B:W.116, B:F.138 Hydrogen bonds: B:N.32, B:D.118 pi-Stacking: B:W.116, B:W.116, B:W.116, B:F.138

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

SO4.4: 10 residues within 4Å: Chain A: H.159, H.160, H.161, H.162, H.163 Chain B: H.160, H.161, H.162, H.163 Ligands: SO4.8 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:H.159, B:H.161, B:H.162, A:H.161, A:H.162 Salt bridges: B:H.160, B:H.161, B:H.162, A:H.160, A:H.161, A:H.162 SO4.8: 10 residues within 4Å: Chain A: H.160, H.161, H.162, H.163 Chain B: H.159, H.160, H.161, H.162, H.163 Ligands: SO4.4 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:H.161, B:H.162, A:H.159, A:H.161, A:H.162 Salt bridges: B:H.160, B:H.161, B:H.162, A:H.160, A:H.161, A:H.162

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yokoyama, T. et al., Discovery of a new class of MTH1 inhibitor by X-ray crystallographic screening. Eur J Med Chem (2019)

Release Date

2019-03-06

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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