SMTL ID : 8tcy.1

Structure of PYCR1 complexed with 7-fluoro-2-oxo-1,2,3,4-tetrahydroquinoline-6-carboxylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-10-mer

Ligands

4 x ZRE: 7-fluoro-2-oxo-1,2,3,4-tetrahydroquinoline-6-carboxylic acid(Non-covalent)

ZRE.1: 12 residues within 4Å: Chain A: L.33, C.117, A.119, C.142, M.143, T.144, G.197, S.198 Chain B: S.255, G.258, A.259, T.260 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.33, A:A.119 Hydrogen bonds: A:T.144, A:T.144, B:S.255, B:A.259, B:T.260 Halogen bonds: A:S.198 ZRE.4: 14 residues within 4Å: Chain C: V.253, S.255, G.258, A.259, T.260 Chain D: L.33, C.117, A.119, C.142, M.143, T.144, G.197, S.198 Ligands: SO4.3 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:S.255, C:A.259, C:T.260, C:T.260, D:T.144, D:T.144 Water bridges: C:I.261 Hydrophobic interactions: D:L.33 ZRE.8: 12 residues within 4Å: Chain F: L.33, C.117, A.119, C.142, M.143, T.144, G.197, S.198 Chain G: S.255, G.258, A.259, T.260 9 PLIP interactions: 4 interactions with chain G, 5 interactions with chain F Hydrogen bonds: G:S.255, G:A.259, G:T.260, G:T.260, F:T.144, F:T.144 Hydrophobic interactions: F:L.33, F:A.119 Halogen bonds: F:S.198 ZRE.11: 14 residues within 4Å: Chain H: V.253, S.255, G.258, A.259, T.260 Chain I: L.33, C.117, A.119, C.142, M.143, T.144, G.197, S.198 Ligands: SO4.10 7 PLIP interactions: 4 interactions with chain H, 3 interactions with chain I Hydrogen bonds: H:S.255, H:A.259, H:T.260, I:T.144, I:T.144 Water bridges: H:I.261 Hydrophobic interactions: I:L.33

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

SO4.2: 5 residues within 4Å: Chain A: V.253, S.255, G.258, A.259, T.260 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.255, A:S.255, A:S.255, A:T.260, A:T.260 Water bridges: A:A.259, A:I.261 SO4.3: 6 residues within 4Å: Chain C: V.253, S.255, G.258, A.259, T.260 Ligands: ZRE.4 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.255, C:A.259, C:T.260, C:T.260 Water bridges: C:G.258 SO4.5: 5 residues within 4Å: Chain D: V.253, S.255, G.258, A.259, T.260 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:S.255, D:S.255, D:A.259, D:T.260, D:T.260 Water bridges: D:G.258, D:G.258, D:T.260, D:T.260 SO4.6: 5 residues within 4Å: Chain E: V.253, S.255, G.258, A.259, T.260 7 PLIP interactions: 7 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:I.261 SO4.9: 5 residues within 4Å: Chain F: V.253, S.255, G.258, A.259, T.260 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:S.255, F:S.255, F:S.255, F:T.260 Water bridges: F:A.259, F:I.261 SO4.10: 6 residues within 4Å: Chain H: V.253, S.255, G.258, A.259, T.260 Ligands: ZRE.11 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:S.255, H:A.259, H:T.260 Water bridges: H:G.258 SO4.12: 5 residues within 4Å: Chain I: V.253, S.255, G.258, A.259, T.260 8 PLIP interactions: 8 interactions with chain I Hydrogen bonds: I:S.255, I:S.255, I:A.259, I:T.260, I:T.260, I:T.260 Water bridges: I:G.258, I:G.258 SO4.13: 5 residues within 4Å: Chain J: V.253, 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, J:T.260 Water bridges: J:I.261

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.7: 6 residues within 4Å: Chain E: K.237, H.241 Chain J: A.43, V.149, V.150, R.151 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.237 PEG.14: 6 residues within 4Å: Chain E: A.43, V.149, V.150, R.151 Chain J: K.237, H.241 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:K.237

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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