SMTL ID : 9gzv.1

Crystal structure of human NUDT14 in complex with a potent inhibitor (MA-955-9)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

3 x 01: 1-(1-methylpiperidin-4-yl)-3-(3-phenoxyphenyl)pyrazolo[3,4-d]pyrimidin-4-amine

01.1: 15 residues within 4Å: Chain A: Y.18, S.43, R.63, A.106, G.107, L.108, E.176, E.178 Chain B: S.34, W.35, D.36, G.148, L.149 Ligands: DMS.9, ACY.12 16 PLIP interactions: 7 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:Y.18, A:A.106, A:L.108, B:W.35, B:W.35, B:L.149, B:L.149 Salt bridges: A:E.176, A:E.178 pi-Stacking: A:Y.18, A:Y.18, B:W.35, B:W.35, B:W.35 Hydrogen bonds: B:D.36, B:D.36 01.6: 8 residues within 4Å: Chain A: E.118, C.121, H.131, L.132, A.133, P.134, D.136, Q.165 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.118 Salt bridges: A:D.136 pi-Stacking: A:H.131 01.10: 10 residues within 4Å: Chain A: W.35, D.36, G.148, L.149 Chain B: Y.18, S.43, R.63, A.106, G.107, L.108 13 PLIP interactions: 6 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:Y.18, B:A.106, B:L.108, B:L.108, A:W.35, A:L.149 pi-Stacking: B:Y.18, B:Y.18, A:W.35, A:W.35, A:W.35 Hydrogen bonds: A:D.36, A:D.36

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 2 residues within 4Å: Chain A: F.75, P.92 No protein-ligand interaction detected (PLIP)

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.3: 3 residues within 4Å: Chain A: S.1, M.2, L.179 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.2 ACY.12: 3 residues within 4Å: Chain B: K.33, S.34 Ligands: 01.1 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.34

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 5 residues within 4Å: Chain A: L.213, P.218, D.221 Ligands: PEG.5, DMS.8 No protein-ligand interaction detected (PLIP) PEG.5: 4 residues within 4Å: Chain A: Q.191, L.213 Ligands: PEG.4, DMS.8 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.191 PEG.11: 5 residues within 4Å: Chain B: H.184, L.185, P.186, F.193 Ligands: DMS.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.184

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 2 residues within 4Å: Chain A: A.106, E.127 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:A.106, A:E.127, H2O.2, H2O.2, H2O.2

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.8: 2 residues within 4Å: Ligands: PEG.4, PEG.5 No protein-ligand interaction detected (PLIP) DMS.9: 7 residues within 4Å: Chain A: T.45, E.103, L.104, Q.154, T.202, G.204 Ligands: 01.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.104 DMS.13: 1 residues within 4Å: Ligands: PEG.11 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Balikci, E. et al., Crystal structure of human NUDT14 in complex with an inhibitor (MA-955-9). To Be Published

Release Date

2025-10-15

Peptides

Uridine diphosphate glucose pyrophosphatase NUDT14: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Uridine diphosphate glucose pyrophosphatase NUDT14

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