SMTL ID : 6aa5.2 (1 other biounit)

Crystal structure of MTH1 in complex with 3-isomangostin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x MKU: 5,9-dihydroxy-8-methoxy-2,2-dimethyl-7-(3-methylbut-2-en-1-yl)-3,4-dihydro-2H,6H-pyrano[3,2-b]xanthen-6-one(Non-covalent)

MKU.1: 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 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.6, A:F.26, A:F.71, A:F.71, A:F.73, A:F.73, A:W.116, A:W.116, A:F.138, A:Q.141 Hydrogen bonds: A:N.32, A:D.118 pi-Stacking: A:W.116, A:W.116, A:W.116, A:F.138, A:F.138 MKU.6: 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 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:Y.6, B:F.26, B:F.71, B:F.71, B:F.73, B:F.73, B:W.116, B:W.116, B:F.138, B:Q.141 Hydrogen bonds: B:N.32, B:D.118 pi-Stacking: B:W.116, B:W.116, B:W.116, B:F.138, B:F.138

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: L.5, D.81, H.83, H.158, H.160 Chain B: H.158 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.81, A:H.83, A:H.158, A:H.160 ZN.3: 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.4: 3 residues within 4Å: Chain A: H.64, C.86, T.87 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.64, A:C.86, H2O.4 ZN.7: 6 residues within 4Å: Chain A: H.158 Chain B: L.5, D.81, H.83, H.158, H.160 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.81, B:H.83, B:H.158, B:H.160 ZN.8: 4 residues within 4Å: Chain A: H.161, H.162 Chain B: E.40, H.163 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Metal complexes: A:H.161, A:H.162, B:E.40, B:E.40, B:H.163 ZN.9: 3 residues within 4Å: Chain B: H.64, C.86, T.87 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.64, B:C.86, H2O.8

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

SO4.5: 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: SO4.10 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:H.161, A:H.162, A:H.163, B:H.161, B:H.162 Salt bridges: A:H.160, A:H.161, A:H.162, B:H.160, B:H.161 SO4.10: 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: SO4.5 10 PLIP interactions: 4 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:H.161, A:H.162, B:H.161, B:H.162, B:H.163 Salt bridges: A:H.160, A:H.161, B:H.160, B:H.161, B: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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