SMTL ID : 7sql.1

Crystal structure of human uridine-cytidine kinase 2 complexed with a weak small molecule inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.1: 8 residues within 4Å: Chain A: Y.65, G.79, F.81, N.82, F.83, D.84, Q.184, F.188 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.79, A:Q.184 PGE.2: 4 residues within 4Å: Chain A: R.66, T.69, Q.72, D.87 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.72, A:D.87

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: T.29, A.30, S.31, G.32, K.33, S.34, S.35, R.169 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:A.30, A:S.31, A:G.32, A:K.33, A:K.33, A:K.33, A:S.34, A:S.35, A:S.35, A:R.169 GOL.6: 8 residues within 4Å: Chain B: G.32, S.35, R.165, R.169, G.211, A.212, D.213 Ligands: PEG.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.35, B:R.169, B:A.212, B:D.213 GOL.9: 7 residues within 4Å: Chain C: T.29, A.30, S.31, G.32, K.33, S.34, S.35 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:A.30, C:G.32, C:K.33, C:K.33, C:S.34, C:S.35, C:S.35 GOL.12: 8 residues within 4Å: Chain D: T.29, A.30, S.31, G.32, K.33, S.34, S.35, R.169 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:A.30, D:G.32, D:K.33, D:K.33, D:K.33, D:S.34, D:S.35, D:S.35, D:R.169

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 9 residues within 4Å: Chain B: Y.65, F.81, N.82, F.83, D.84, F.114, R.166, Q.184, F.188 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.79, B:F.83 PG4.11: 9 residues within 4Å: Chain D: G.79, F.81, N.82, F.83, D.84, R.176, Q.180, Q.184, F.188 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.180, D:Q.184

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

PEG.5: 9 residues within 4Å: Chain B: T.29, A.30, S.31, G.32, K.33, S.34, S.35, R.169 Ligands: GOL.6 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:A.30, B:S.31, B:G.32, B:K.33, B:S.34, B:S.35, B:S.35, B:R.169, B:R.169 PEG.8: 5 residues within 4Å: Chain C: Y.65, F.83, F.114, R.174, R.176 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.65, C:R.174 PEG.13: 5 residues within 4Å: Chain D: Q.61, P.86, F.89, N.91, I.94 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.61 Water bridges: D:R.66, D:N.91, D:L.138

2 x AQX: N-(4-bromophenyl)-2-{[1-(4-fluorophenyl)-4-oxo-4,5-dihydro-1H-pyrazolo[3,4-d]pyrimidin-6-yl]sulfanyl}acetamide(Non-covalent)

AQX.7: 10 residues within 4Å: Chain A: D.158, A.159, D.160, E.194 Chain B: K.201 Chain C: D.158, A.159, D.160, E.194, L.198 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:D.158, C:A.159 Hydrogen bonds: C:A.159, C:D.160, A:A.159, A:D.160 Water bridges: A:Y.185 AQX.10: 10 residues within 4Å: Chain B: D.158, A.159, D.160, E.194 Chain C: K.202 Chain D: D.158, A.159, D.160, E.194, L.198 7 PLIP interactions: 5 interactions with chain D, 1 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: D:A.159, D:L.198 Hydrogen bonds: D:D.158, D:A.159, D:D.160, B:A.159 Halogen bonds: C:K.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mashayekh, S. et al., Structure-Based Prototyping of Allosteric Inhibitors of Human Uridine/Cytidine Kinase 2 (UCK2). Biochemistry (2022)

Release Date

2022-10-12

Peptides

Uridine-cytidine kinase 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Uridine-cytidine kinase 2

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