SMTL ID : 7miv.1

Mouse CTPS2-I250T bound to inhibitor R80

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x GLN: GLUTAMINE(Non-covalent)

GLN.1: 13 residues within 4Å: Chain A: G.371, G.372, F.373, G.374, C.399, L.400, Q.403, E.423, R.479, H.480, R.481, Y.482, H.526 11 PLIP interactions: 9 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:F.373, A:L.400 Hydrogen bonds: A:G.372, A:G.372, A:L.400, A:Q.403, A:R.479, A:R.481, A:Y.482, Q.1, Q.1 GLN.5: 13 residues within 4Å: Chain B: G.371, G.372, F.373, G.374, C.399, L.400, Q.403, E.423, R.479, H.480, R.481, Y.482, H.526 10 PLIP interactions: 9 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:F.373 Hydrogen bonds: B:G.372, B:L.400, B:Q.403, B:Q.403, B:E.423, B:R.479, B:R.481, B:Y.482, Q.5 GLN.9: 13 residues within 4Å: Chain C: G.371, G.372, F.373, G.374, C.399, L.400, Q.403, E.423, R.479, H.480, R.481, Y.482, H.526 11 PLIP interactions: 10 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:F.373, C:L.400 Hydrogen bonds: C:G.372, C:G.372, C:L.400, C:Q.403, C:Q.403, C:R.479, C:R.481, C:Y.482, Q.9 GLN.13: 13 residues within 4Å: Chain D: G.371, G.372, F.373, G.374, 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:L.400, D:Q.403, D:E.423, D:R.479, D:R.481, D:Y.482, Q.13, Q.13

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: E.191, K.193, K.229 Ligands: UTP.3 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain B: E.191, K.193, K.229 Ligands: UTP.7 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain C: E.191, K.193, K.229 Ligands: UTP.11 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain D: E.191, K.193, K.229 Ligands: UTP.15 No protein-ligand interaction detected (PLIP)

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

UTP.3: 23 residues within 4Å: Chain A: E.191, Q.192, K.193, T.194, K.195, Q.198, K.229 Chain B: I.11, S.12, K.38, I.39, D.40, P.41, Y.42, H.55, G.148, G.149, T.150, D.153, E.155 Chain D: T.110, Q.112 Ligands: MG.2 18 PLIP interactions: 10 interactions with chain A, 7 interactions with chain B, 1 interactions with chain D Hydrogen bonds: A:T.194, A:T.194, A:K.195, A:Q.198, B:S.12, B:K.38, B:H.55, B:G.149, B:D.153, B:D.153, D:Q.112 Salt bridges: A:K.193, A:K.193, A:K.195, A:K.195, A:K.229, A:K.229 Hydrophobic interactions: B:D.40 UTP.7: 23 residues within 4Å: Chain A: I.11, S.12, K.38, I.39, D.40, P.41, Y.42, H.55, G.148, G.149, T.150, D.153, E.155 Chain B: E.191, Q.192, K.193, T.194, K.195, Q.198, K.229 Chain C: T.110, Q.112 Ligands: MG.8 17 PLIP interactions: 6 interactions with chain A, 10 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: A:D.40 Hydrogen bonds: A:S.12, A:K.38, A:H.55, A:G.149, A:D.153, B:T.194, B:T.194, B:K.195, B:Q.198, C:Q.112 Salt bridges: B:K.193, B:K.193, B:K.195, B:K.195, B:K.229, B:K.229 UTP.11: 23 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: I.11, S.12, K.38, I.39, D.40, P.41, Y.42, H.55, G.148, G.149, T.150, D.153, E.155 Ligands: MG.10 17 PLIP interactions: 10 interactions with chain C, 1 interactions with chain B, 6 interactions with chain D Hydrogen bonds: C:T.194, C:T.194, C:K.195, C:Q.198, B:Q.112, D:S.12, D:K.38, D:H.55, D:G.149, D:D.153 Salt bridges: C:K.193, C:K.193, C:K.195, C:K.195, C:K.229, C:K.229 Hydrophobic interactions: D:D.40 UTP.15: 23 residues within 4Å: Chain A: T.110, Q.112 Chain C: I.11, S.12, K.38, I.39, D.40, P.41, Y.42, H.55, G.148, G.149, T.150, D.153, E.155 Chain D: E.191, Q.192, K.193, T.194, K.195, Q.198, K.229 Ligands: MG.16 19 PLIP interactions: 11 interactions with chain D, 7 interactions with chain C, 1 interactions with chain A Hydrogen bonds: D:E.191, D:T.194, D:T.194, D:K.195, D:Q.198, C:S.12, C:K.38, C:H.55, C:G.149, C:D.153, C:D.153, A:Q.112 Salt bridges: D:K.193, D:K.193, D:K.195, D:K.195, D:K.229, D:K.229 Hydrophobic interactions: C:D.40

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

ZG4.4: 24 residues within 4Å: Chain A: I.14, G.15, I.18, I.19, N.73, R.76, F.77, R.217, I.244, H.245, D.246, V.247, S.248, S.249, T.250, Y.251, V.253, W.285, Y.292, F.318, K.319, E.322, H.323, P.533 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.19, A:F.77, A:T.250, A:Y.251, A:V.253, A:W.285, A:W.285, A:F.318, A:E.322, A:P.533 Hydrogen bonds: A:V.247, A:T.250, A:T.250, A:K.319, A:H.323 ZG4.6: 24 residues within 4Å: Chain B: I.14, G.15, I.18, I.19, N.73, R.76, F.77, R.217, I.244, H.245, D.246, V.247, S.248, S.249, T.250, Y.251, V.253, W.285, Y.292, F.318, K.319, E.322, H.323, P.533 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:I.19, B:F.77, B:T.250, B:Y.251, B:V.253, B:W.285, B:W.285, B:F.318, B:E.322, B:P.533 Hydrogen bonds: B:D.246, B:V.247, B:T.250, B:T.250, B:K.319, B:H.323 ZG4.12: 24 residues within 4Å: Chain C: I.14, G.15, I.18, I.19, N.73, R.76, F.77, R.217, I.244, H.245, D.246, V.247, S.248, S.249, T.250, Y.251, V.253, W.285, Y.292, F.318, K.319, E.322, H.323, P.533 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:I.19, C:F.77, C:T.250, C:Y.251, C:V.253, C:W.285, C:W.285, C:F.318, C:E.322, C:P.533 Hydrogen bonds: C:D.246, C:V.247, C:T.250, C:T.250, C:K.319, C:H.323 ZG4.14: 24 residues within 4Å: Chain D: I.14, G.15, I.18, I.19, N.73, R.76, F.77, R.217, I.244, H.245, D.246, V.247, S.248, S.249, T.250, Y.251, V.253, W.285, Y.292, F.318, K.319, E.322, H.323, P.533 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:I.19, D:F.77, D:T.250, D:Y.251, D:V.253, D:W.285, D:W.285, D:F.318, D:E.322, D:P.533 Hydrogen bonds: D:V.247, D:T.250, D:T.250, D:K.319, D:H.323

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