SMTL ID : 7miu.1

Mouse CTPS2 bound to inhibitor R80

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x GLN: GLUTAMINE(Non-covalent)

GLN.1: 12 residues within 4Å: Chain A: G.371, G.372, F.373, C.399, L.400, Q.403, E.423, R.479, H.480, R.481, Y.482, H.526 10 PLIP interactions: 8 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:F.373 Hydrogen bonds: A:G.372, A:L.400, A:Q.403, A:E.423, A:R.479, A:R.481, A:Y.482, Q.1, Q.1 GLN.5: 12 residues within 4Å: Chain B: G.371, G.372, F.373, C.399, L.400, Q.403, E.423, R.479, H.480, R.481, Y.482, H.526 9 PLIP interactions: 9 interactions with chain B, Hydrophobic interactions: B:F.373 Hydrogen bonds: B:G.372, B:G.372, B:L.400, B:Q.403, B:Q.403, B:R.479, B:R.481, B:Y.482 GLN.9: 12 residues within 4Å: Chain C: G.371, G.372, F.373, C.399, L.400, Q.403, E.423, R.479, H.480, R.481, Y.482, H.526 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.373 Hydrogen bonds: C:G.372, C:L.400, C:Q.403, C:Q.403, C:E.423, C:R.479, C:R.481, C:Y.482 GLN.13: 12 residues within 4Å: Chain D: G.371, G.372, F.373, C.399, L.400, Q.403, E.423, R.479, H.480, R.481, Y.482, H.526 10 PLIP interactions: 8 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: D:F.373 Hydrogen bonds: D:G.372, D:G.372, D:L.400, D:Q.403, D:R.479, D:R.481, D:Y.482, Q.13, Q.13

4 x ZG4: N-(1-{2-[(cyclopropanesulfonyl)amino]-1,3-thiazol-4-yl}cyclopropyl)-5-(6-ethoxypyrazin-2-yl)pyridine-2-carboxamide(Non-covalent)

ZG4.2: 20 residues within 4Å: Chain A: G.15, I.18, I.19, N.73, R.76, F.77, R.217, I.244, H.245, D.246, V.247, I.250, Y.251, V.253, W.285, F.318, K.319, E.322, H.323, P.533 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.19, A:F.77, A:I.250, A:I.250, A:Y.251, A:V.253, A:W.285, A:F.318, A:E.322, A:P.533 Hydrogen bonds: A:V.247, A:I.250, A:K.319, A:K.319 ZG4.8: 20 residues within 4Å: Chain B: G.15, I.18, I.19, N.73, R.76, F.77, R.217, I.244, H.245, D.246, V.247, I.250, Y.251, V.253, W.285, F.318, K.319, E.322, H.323, P.533 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:I.19, B:F.77, B:I.250, B:I.250, B:Y.251, B:V.253, B:W.285, B:F.318, B:E.322, B:P.533 Hydrogen bonds: B:V.247, B:I.250, B:K.319, B:K.319 ZG4.10: 20 residues within 4Å: Chain C: G.15, I.18, I.19, N.73, R.76, F.77, R.217, I.244, H.245, D.246, V.247, I.250, Y.251, V.253, W.285, F.318, K.319, E.322, H.323, P.533 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:I.19, C:F.77, C:I.250, C:I.250, C:Y.251, C:V.253, C:W.285, C:F.318, C:E.322, C:P.533 Hydrogen bonds: C:D.246, C:V.247, C:I.250, C:K.319, C:K.319 ZG4.16: 20 residues within 4Å: Chain D: G.15, I.18, I.19, N.73, R.76, F.77, R.217, I.244, H.245, D.246, V.247, I.250, Y.251, V.253, W.285, F.318, K.319, E.322, H.323, P.533 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:I.19, D:F.77, D:I.250, D:I.250, D:Y.251, D:V.253, D:W.285, D:F.318, D:E.322, D:P.533 Hydrogen bonds: D:V.247, D:I.250, D:K.319, D:K.319

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: E.191, K.193 Ligands: UTP.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.191, A:E.191 MG.7: 3 residues within 4Å: Chain B: E.191, K.193 Ligands: UTP.6 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.191, B:E.191 MG.11: 3 residues within 4Å: Chain C: E.191, K.193 Ligands: UTP.12 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.191, C:E.191 MG.15: 3 residues within 4Å: Chain D: E.191, K.193 Ligands: UTP.14 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:E.191, D:E.191

4 x UTP: URIDINE 5'-TRIPHOSPHATE(Non-covalent)

UTP.4: 19 residues within 4Å: Chain A: E.191, Q.192, K.193, T.194, K.195, Q.198, K.229 Chain B: S.12, K.38, D.40, P.41, Y.42, H.55, G.148, G.149, D.153 Chain D: T.110, Q.112 Ligands: MG.3 16 PLIP interactions: 10 interactions with chain A, 5 interactions with chain B, 1 interactions with chain D Hydrogen bonds: A:T.194, A:K.195, A:Q.198, B:S.12, B:K.38, B:G.149, B:D.153, D:Q.112 Salt bridges: A:K.193, A:K.193, A:K.193, A:K.195, A:K.195, A:K.229, A:K.229 Hydrophobic interactions: B:D.40 UTP.6: 19 residues within 4Å: Chain A: S.12, K.38, D.40, P.41, Y.42, H.55, G.148, G.149, D.153 Chain B: E.191, Q.192, K.193, T.194, K.195, Q.198, K.229 Chain C: T.110, Q.112 Ligands: MG.7 17 PLIP interactions: 12 interactions with chain B, 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:E.191, B:T.194, B:T.194, B:K.195, B:Q.198, A:S.12, A:K.38, A:G.149, C:Q.112 Salt bridges: B:K.193, B:K.193, B:K.193, B:K.195, B:K.195, B:K.229, B:K.229 Hydrophobic interactions: A:D.40 UTP.12: 19 residues within 4Å: Chain B: T.110, Q.112 Chain C: E.191, Q.192, K.193, T.194, K.195, Q.198, K.229 Chain D: S.12, K.38, D.40, P.41, Y.42, H.55, G.148, G.149, D.153 Ligands: MG.11 17 PLIP interactions: 12 interactions with chain C, 4 interactions with chain D, 1 interactions with chain B Hydrogen bonds: C:E.191, C:T.194, C:T.194, C:K.195, C:Q.198, D:S.12, D:K.38, D:G.149, B:Q.112 Salt bridges: C:K.193, C:K.193, C:K.193, C:K.195, C:K.195, C:K.229, C:K.229 Hydrophobic interactions: D:D.40 UTP.14: 19 residues within 4Å: Chain A: T.110, Q.112 Chain C: S.12, K.38, D.40, P.41, Y.42, H.55, G.148, G.149, D.153 Chain D: E.191, Q.192, K.193, T.194, K.195, Q.198, K.229 Ligands: MG.15 16 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A, 10 interactions with chain D Hydrophobic interactions: C:D.40 Hydrogen bonds: C:S.12, C:K.38, C:G.149, C:D.153, A:Q.112, D:T.194, D:K.195, D:Q.198 Salt bridges: D:K.193, D:K.193, D:K.193, D:K.195, D:K.195, D:K.229, D:K.229

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lynch, E.M. et al., Structural basis for isoform-specific inhibition of human CTPS1. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-10-13

Peptides

CTP synthase 2: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
C

C
H

D
G

CTP synthase 2