SMTL ID : 7mig.1

Human CTPS1 bound to inhibitor T35

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

4 x ZFY: 2-{2-[(cyclopropanesulfonyl)amino]-1,3-thiazol-4-yl}-2-methyl-N-{5-[6-(trifluoromethyl)pyrazin-2-yl]pyridin-2-yl}propanamide(Non-covalent)

ZFY.1: 23 residues within 4Å: Chain A: G.15, I.18, I.19, N.73, R.76, F.77, R.217, V.244, H.245, D.246, V.247, S.248, S.249, I.250, Y.251, V.253, W.285, Y.292, I.318, K.319, E.322, H.323, P.533 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:R.76, A:F.77, A:F.77, A:I.250, A:W.285, A:Y.292, A:E.322, A:P.533 Hydrogen bonds: A:R.76, A:V.247, A:I.250, A:K.319, A:H.323 ZFY.7: 23 residues within 4Å: Chain B: G.15, I.18, I.19, N.73, R.76, F.77, R.217, V.244, H.245, D.246, V.247, S.248, S.249, I.250, Y.251, V.253, W.285, Y.292, I.318, K.319, E.322, H.323, P.533 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:R.76, B:F.77, B:F.77, B:I.250, B:W.285, B:Y.292, B:E.322, B:P.533 Hydrogen bonds: B:R.76, B:V.247, B:I.250, B:K.319, B:H.323 ZFY.9: 23 residues within 4Å: Chain C: G.15, I.18, I.19, N.73, R.76, F.77, R.217, V.244, H.245, D.246, V.247, S.248, S.249, I.250, Y.251, V.253, W.285, Y.292, I.318, K.319, E.322, H.323, P.533 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:R.76, C:F.77, C:F.77, C:I.250, C:W.285, C:Y.292, C:E.322, C:P.533 Hydrogen bonds: C:R.76, C:V.247, C:I.250, C:K.319, C:H.323 ZFY.15: 23 residues within 4Å: Chain D: G.15, I.18, I.19, N.73, R.76, F.77, R.217, V.244, H.245, D.246, V.247, S.248, S.249, I.250, Y.251, V.253, W.285, Y.292, I.318, K.319, E.322, H.323, P.533 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:R.76, D:F.77, D:F.77, D:I.250, D:W.285, D:Y.292, D:E.322, D:P.533 Hydrogen bonds: D:R.76, D:V.247, D:I.250, D:K.319, D:H.323

4 x GLN: GLUTAMINE(Non-covalent)

GLN.2: 15 residues within 4Å: Chain A: G.371, G.372, F.373, G.374, C.399, L.400, Q.403, E.423, F.424, R.479, H.480, R.481, F.482, Q.524, H.526 12 PLIP interactions: 10 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:H.480, A:R.481, A:F.482, A:H.526, Q.2, Q.2 GLN.8: 15 residues within 4Å: Chain B: G.371, G.372, F.373, G.374, C.399, L.400, Q.403, E.423, F.424, R.479, H.480, R.481, F.482, Q.524, H.526 12 PLIP interactions: 11 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:F.373, B:L.400 Hydrogen bonds: B:G.372, B:G.372, B:L.400, B:Q.403, B:Q.403, B:H.480, B:R.481, B:F.482, B:H.526, Q.8 GLN.10: 15 residues within 4Å: Chain C: G.371, G.372, F.373, G.374, C.399, L.400, Q.403, E.423, F.424, R.479, H.480, R.481, F.482, Q.524, H.526 12 PLIP interactions: 11 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:H.480, C:R.481, C:F.482, C:H.526, Q.10 GLN.16: 15 residues within 4Å: Chain D: G.371, G.372, F.373, G.374, C.399, L.400, Q.403, E.423, F.424, R.479, H.480, R.481, F.482, Q.524, H.526 12 PLIP interactions: 10 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: D:F.373, D:L.400 Hydrogen bonds: D:G.372, D:G.372, D:L.400, D:Q.403, D:H.480, D:R.481, D:F.482, D:H.526, Q.16, Q.16

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: K.193, K.229 Ligands: UTP.4 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain B: K.193, K.229 Ligands: UTP.6 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain C: K.193, K.229 Ligands: UTP.12 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain D: K.193, K.229 Ligands: UTP.14 No protein-ligand interaction detected (PLIP)

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

UTP.4: 21 residues within 4Å: Chain A: Q.192, K.193, T.194, K.195, Q.198, K.229 Chain B: I.11, S.12, K.16, K.38, I.39, D.40, P.41, Y.42, H.55, G.148, G.149, E.155 Chain D: T.110, Q.112 Ligands: MG.3 16 PLIP interactions: 9 interactions with chain A, 7 interactions with chain B Hydrogen bonds: A:T.194, A:K.195, A:K.195, A:Q.198, B:S.12, B:S.12, B:K.38, B:P.41, B:H.55, B:G.149 Salt bridges: A:K.193, A:K.193, A:K.195, A:K.195, A:K.229 Hydrophobic interactions: B:D.40 UTP.6: 21 residues within 4Å: Chain A: I.11, S.12, K.16, K.38, I.39, D.40, P.41, Y.42, H.55, G.148, G.149, E.155 Chain B: Q.192, K.193, T.194, K.195, Q.198, K.229 Chain C: T.110, Q.112 Ligands: MG.5 15 PLIP interactions: 6 interactions with chain A, 9 interactions with chain B Hydrophobic interactions: A:D.40 Hydrogen bonds: A:S.12, A:K.38, A:P.41, A:H.55, A:G.149, B:T.194, B:K.195, B:K.195, B:Q.198 Salt bridges: B:K.193, B:K.193, B:K.195, B:K.195, B:K.229 UTP.12: 21 residues within 4Å: Chain B: T.110, Q.112 Chain C: Q.192, K.193, T.194, K.195, Q.198, K.229 Chain D: I.11, S.12, K.16, K.38, I.39, D.40, P.41, Y.42, H.55, G.148, G.149, E.155 Ligands: MG.11 15 PLIP interactions: 9 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:T.194, C:K.195, C:K.195, C:Q.198, D:S.12, D:K.38, D:P.41, D:H.55, D:G.149 Salt bridges: C:K.193, C:K.193, C:K.195, C:K.195, C:K.229 Hydrophobic interactions: D:D.40 UTP.14: 21 residues within 4Å: Chain A: T.110, Q.112 Chain C: I.11, S.12, K.16, K.38, I.39, D.40, P.41, Y.42, H.55, G.148, G.149, E.155 Chain D: Q.192, K.193, T.194, K.195, Q.198, K.229 Ligands: MG.13 16 PLIP interactions: 9 interactions with chain D, 7 interactions with chain C Hydrogen bonds: D:T.194, D:K.195, D:K.195, D:Q.198, C:S.12, C:S.12, C:K.38, C:P.41, C:H.55, C:G.149 Salt bridges: D:K.193, D:K.193, D:K.195, D:K.195, D:K.229 Hydrophobic interactions: C:D.40

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 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

D
E

CTP synthase 1

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