SMTL ID : 7mih.1

Human CTPS2 bound to inhibitor R80

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

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

ZG4.1: 25 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, M.288, Y.292, F.318, K.319, E.322, H.323, P.533 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.18, A:I.19, A:F.77, A:I.244, A:T.250, A:Y.251, A:W.285, A:F.318, A:E.322, A:P.533 Hydrogen bonds: A:R.76, A:V.247, A:T.250, A:T.250, A:T.250, A:K.319, A:H.323 ZG4.6: 25 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, M.288, Y.292, F.318, K.319, E.322, H.323, P.533 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:I.18, B:I.19, B:F.77, B:I.244, B:T.250, B:Y.251, B:W.285, B:F.318, B:E.322, B:P.533 Hydrogen bonds: B:R.76, B:V.247, B:T.250, B:T.250, B:T.250, B:K.319, B:H.323 ZG4.9: 25 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, M.288, Y.292, F.318, K.319, E.322, H.323, P.533 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:I.18, C:I.19, C:F.77, C:I.244, C:T.250, C:Y.251, C:W.285, C:F.318, C:E.322, C:P.533 Hydrogen bonds: C:R.76, C:V.247, C:T.250, C:T.250, C:T.250, C:K.319, C:H.323 ZG4.14: 25 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, M.288, Y.292, F.318, K.319, E.322, H.323, P.533 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:I.18, D:I.19, D:F.77, D:I.244, D:T.250, D:Y.251, D:W.285, D:F.318, D:E.322, D:P.533 Hydrogen bonds: D:R.76, D:V.247, D:T.250, D:T.250, D:T.250, D:K.319, D:H.323

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

UTP.2: 23 residues within 4Å: Chain A: I.11, S.12, K.16, K.38, D.40, P.41, Y.42, H.55, G.148, G.149, T.150, D.153, E.155 Chain B: Q.192, K.193, T.194, K.195, Q.198, K.229, F.233 Chain C: T.110, Q.112 Ligands: MG.5 19 PLIP interactions: 1 interactions with chain C, 9 interactions with chain B, 9 interactions with chain A Hydrogen bonds: C:Q.112, B:T.194, B:K.195, B:Q.198, A:S.12, A:K.38, A:D.40, A:D.40, A:Y.42, A:H.55, A:G.149, A:D.153 Salt bridges: B:K.193, B:K.193, B:K.195, B:K.195, B:K.229, B:K.229 pi-Stacking: A:H.55 UTP.7: 23 residues within 4Å: Chain A: Q.192, K.193, T.194, K.195, Q.198, K.229, F.233 Chain B: I.11, S.12, K.16, K.38, 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.4 18 PLIP interactions: 8 interactions with chain B, 9 interactions with chain A, 1 interactions with chain D Hydrogen bonds: B:S.12, B:K.38, B:D.40, B:Y.42, B:H.55, B:G.149, B:D.153, A:T.194, A:K.195, A:Q.198, D:Q.112 pi-Stacking: B:H.55 Salt bridges: A:K.193, A:K.193, A:K.195, A:K.195, A:K.229, A:K.229 UTP.10: 23 residues within 4Å: Chain A: T.110, Q.112 Chain C: I.11, S.12, K.16, K.38, D.40, P.41, Y.42, H.55, G.148, G.149, T.150, D.153, E.155 Chain D: Q.192, K.193, T.194, K.195, Q.198, K.229, F.233 Ligands: MG.13 18 PLIP interactions: 8 interactions with chain C, 1 interactions with chain A, 9 interactions with chain D Hydrogen bonds: C:S.12, C:K.38, C:D.40, C:Y.42, C:H.55, C:G.149, C:D.153, A:Q.112, D:T.194, D:K.195, D:Q.198 pi-Stacking: C:H.55 Salt bridges: D:K.193, D:K.193, D:K.195, D:K.195, D:K.229, D:K.229 UTP.15: 23 residues within 4Å: Chain B: T.110, Q.112 Chain C: Q.192, K.193, T.194, K.195, Q.198, K.229, F.233 Chain D: I.11, S.12, K.16, K.38, D.40, P.41, Y.42, H.55, G.148, G.149, T.150, D.153, E.155 Ligands: MG.12 19 PLIP interactions: 9 interactions with chain C, 9 interactions with chain D, 1 interactions with chain B Hydrogen bonds: C:T.194, C:K.195, C:Q.198, D:S.12, D:K.38, D:D.40, D:D.40, D:Y.42, D:H.55, D:G.149, D:D.153, B:Q.112 Salt bridges: C:K.193, C:K.193, C:K.195, C:K.195, C:K.229, C:K.229 pi-Stacking: D:H.55

4 x GLN: GLUTAMINE(Non-covalent)

GLN.3: 12 residues within 4Å: Chain A: G.371, G.372, F.373, C.399, L.400, Q.403, R.479, H.480, R.481, F.482, Q.524, 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:G.372, A:L.400, A:Q.403, A:R.481, A:F.482, A:H.526, Q.3, Q.3 GLN.8: 12 residues within 4Å: Chain B: G.371, G.372, F.373, C.399, L.400, Q.403, R.479, H.480, R.481, F.482, Q.524, 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:G.372, B:L.400, B:Q.403, B:Q.403, B:R.481, B:F.482, B:H.526, Q.8 GLN.11: 12 residues within 4Å: Chain C: G.371, G.372, F.373, C.399, L.400, Q.403, R.479, H.480, R.481, F.482, Q.524, H.526 10 PLIP interactions: 1 Ligand-Ligand interactions, 9 interactions with chain C Hydrogen bonds: Q.11, C:G.372, C:G.372, C:L.400, C:Q.403, C:Q.403, C:R.481, C:F.482, C:H.526 Hydrophobic interactions: C:F.373 GLN.16: 12 residues within 4Å: Chain D: G.371, G.372, F.373, C.399, L.400, Q.403, R.479, H.480, R.481, F.482, Q.524, 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.481, D:F.482, D:H.526, Q.16, Q.16

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: K.193, K.229 Ligands: UTP.7 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: K.193, K.229 Ligands: UTP.2 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain C: K.193, K.229 Ligands: UTP.15 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain D: K.193, K.229 Ligands: UTP.10 No protein-ligand interaction detected (PLIP)

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
A

B
B

C
C

D
E

CTP synthase 2

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