SMTL ID : 8tcx.1

Structure of PYCR1 complexed with 2,4-dioxo-1,2,3,4-tetrahydroquinazoline-6-carboxylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-10-mer

Ligands

8 x ZR9: 2,4-dioxo-1,2,3,4-tetrahydroquinazoline-6-carboxylic acid(Non-covalent)

ZR9.1: 12 residues within 4Å: Chain A: L.33, C.117, A.118, A.119, M.143, T.144, G.197 Chain B: V.253, S.255, G.258, A.259, T.260 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:C.117, A:A.119, A:T.144, A:T.144, B:A.259, B:T.260 Water bridges: B:S.255, B:G.258 ZR9.4: 12 residues within 4Å: Chain A: V.253, S.255, G.258, A.259, T.260 Chain B: L.33, C.117, A.119, M.143, T.144, G.197 Ligands: SO4.3 12 PLIP interactions: 4 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:C.117, B:A.119, B:T.144, B:T.144, A:S.255, A:A.259, A:T.260, A:T.260, A:T.260 Water bridges: A:S.255, A:G.258, A:I.261 ZR9.5: 11 residues within 4Å: Chain C: L.33, C.117, A.118, A.119, M.143, T.144, G.197 Chain D: S.255, A.259, T.260 Ligands: SO4.7 10 PLIP interactions: 5 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:A.119 Hydrogen bonds: C:C.117, C:A.119, C:T.144, C:T.144, D:S.255, D:A.259, D:T.260 Water bridges: D:G.258, D:I.261 ZR9.6: 10 residues within 4Å: Chain C: G.258, A.259, T.260 Chain D: L.33, C.117, A.118, A.119, M.143, T.144, G.197 11 PLIP interactions: 5 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:A.119 Hydrogen bonds: D:C.117, D:A.119, D:T.144, D:T.144, C:A.259, C:T.260, C:T.260, C:T.260 Water bridges: C:S.255, C:G.258 ZR9.9: 12 residues within 4Å: Chain F: L.33, C.117, A.118, A.119, M.143, T.144, G.197 Chain G: V.253, S.255, G.258, A.259, T.260 9 PLIP interactions: 4 interactions with chain F, 5 interactions with chain G Hydrogen bonds: F:C.117, F:A.119, F:T.144, F:T.144, G:A.259, G:T.260, G:T.260 Water bridges: G:S.255, G:G.258 ZR9.12: 12 residues within 4Å: Chain F: V.253, S.255, G.258, A.259, T.260 Chain G: L.33, C.117, A.119, M.143, T.144, G.197 Ligands: SO4.11 11 PLIP interactions: 7 interactions with chain F, 4 interactions with chain G Hydrogen bonds: F:S.255, F:A.259, F:T.260, F:T.260, G:C.117, G:A.119, G:T.144, G:T.144 Water bridges: F:S.255, F:G.258, F:I.261 ZR9.13: 11 residues within 4Å: Chain H: L.33, C.117, A.118, A.119, M.143, T.144, G.197 Chain I: S.255, A.259, T.260 Ligands: SO4.15 11 PLIP interactions: 6 interactions with chain I, 5 interactions with chain H Hydrogen bonds: I:S.255, I:A.259, I:T.260, I:T.260, H:C.117, H:A.119, H:T.144, H:T.144 Water bridges: I:G.258, I:I.261 Hydrophobic interactions: H:A.119 ZR9.14: 10 residues within 4Å: Chain H: G.258, A.259, T.260 Chain I: L.33, C.117, A.118, A.119, M.143, T.144, G.197 10 PLIP interactions: 5 interactions with chain H, 5 interactions with chain I Hydrogen bonds: H:A.259, H:T.260, H:T.260, I:C.117, I:A.119, I:T.144, I:T.144 Water bridges: H:S.255, H:G.258 Hydrophobic interactions: I:A.119

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: Q.32, L.61, A.62, T.63 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.32, A:A.62, A:T.63 SO4.3: 7 residues within 4Å: Chain A: V.253, S.254, S.255, G.258, A.259, T.260 Ligands: ZR9.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.255, A:S.255, A:S.255, A:A.259, A:T.260, A:T.260 Water bridges: A:I.261 SO4.7: 7 residues within 4Å: Chain D: V.253, S.254, S.255, G.258, A.259, T.260 Ligands: ZR9.5 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:S.255, D:A.259, D:T.260, D:T.260 SO4.8: 6 residues within 4Å: Chain E: V.253, S.254, S.255, G.258, A.259, T.260 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:S.255, E:S.255, E:S.255, E:A.259, E:T.260, E:T.260 Water bridges: E:V.253, E:I.261 SO4.10: 4 residues within 4Å: Chain F: Q.32, L.61, A.62, T.63 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Q.32, F:A.62, F:T.63 SO4.11: 7 residues within 4Å: Chain F: V.253, S.254, S.255, G.258, A.259, T.260 Ligands: ZR9.12 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:S.255, F:S.255, F:S.255, F:A.259, F:T.260 Water bridges: F:I.261 SO4.15: 7 residues within 4Å: Chain I: V.253, S.254, S.255, G.258, A.259, T.260 Ligands: ZR9.13 5 PLIP interactions: 5 interactions with chain I Hydrogen bonds: I:S.255, I:A.259, I:T.260, I:T.260, I:T.260 SO4.16: 6 residues within 4Å: Chain J: V.253, S.254, S.255, G.258, A.259, T.260 7 PLIP interactions: 7 interactions with chain J Hydrogen bonds: J:S.255, J:S.255, J:S.255, J:A.259, J:T.260 Water bridges: J:V.253, J:I.261

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Meeks, K.R. et al., Novel Fragment Inhibitors of PYCR1 from Docking-Guided X-ray Crystallography. J.Chem.Inf.Model. (2024)

Release Date

2024-03-06

Peptides

Pyrroline-5-carboxylate reductase 1, mitochondrial: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
A

G
B

H
C

I
D

J
E

Pyrroline-5-carboxylate reductase 1, mitochondrial

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