SMTL ID : 7y8l.1 (2 other biounits)

Structure of ScIRED-R2-V3 from Streptomyces clavuligerus in complex with 5-(2,5-difluorophenyl)-3,4-dihydro-2H-pyrrole

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-tetramer

Ligands

3 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 27 residues within 4Å: Chain A: G.11, L.12, G.13, P.14, M.15, N.34, R.35, T.36, R.39, S.67, L.68, T.69, A.73, A.76, L.77, L.93, S.94, S.95, V.120, C.122, P.123, P.124, Y.170 Chain B: A.232, R.234, M.237 Ligands: 4IS.2 20 PLIP interactions: 16 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:L.12, A:M.15, A:N.34, A:R.35, A:T.36, A:T.36, A:R.39, A:L.68, A:T.69, A:T.69, A:S.95, A:Y.170, B:A.232 Salt bridges: A:R.35, A:R.39, B:R.234 pi-Cation interactions: A:R.35, A:R.35 Water bridges: B:R.234, B:M.237 NDP.3: 25 residues within 4Å: Chain A: A.232, R.234, M.237 Chain B: G.11, L.12, G.13, P.14, M.15, N.34, R.35, T.36, R.39, S.67, L.68, T.69, A.73, L.77, L.93, S.94, S.95, V.120, C.122, P.124, Y.170 Ligands: 4IS.4 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:L.12, B:G.13, B:M.15, B:N.34, B:T.36, B:R.39, B:R.39, B:L.68, B:T.69, B:S.95, B:Y.170, A:A.232 Water bridges: A:R.234 Salt bridges: A:R.234 NDP.8: 27 residues within 4Å: Chain C: A.232, R.234, M.237 Chain D: G.11, L.12, G.13, P.14, M.15, N.34, R.35, T.36, R.39, S.67, L.68, T.69, A.73, A.76, L.77, L.93, S.94, S.95, V.120, C.122, P.123, P.124, Y.170 Ligands: 4IS.7 18 PLIP interactions: 16 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:L.12, D:M.15, D:N.34, D:R.35, D:R.35, D:R.35, D:T.36, D:T.36, D:L.68, D:T.69, D:T.69, D:S.95, C:A.232 Salt bridges: D:R.35, D:R.39, C:R.234 pi-Cation interactions: D:R.35, D:R.35

4 x 4IS: 5-[2,5-bis(fluoranyl)phenyl]-3,4-dihydro-2~{H}-pyrrole(Non-covalent)

4IS.2: 11 residues within 4Å: Chain A: T.121, C.122, Y.170, M.174, W.177, W.178 Chain B: F.215, Y.219, D.233, F.279 Ligands: NDP.1 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.177, A:W.177, A:W.178, B:F.215 Halogen bonds: A:Y.170, B:Y.219 4IS.4: 12 residues within 4Å: Chain A: F.215, Y.219, D.233 Chain B: V.120, T.121, C.122, P.123, Y.170, M.174, W.177, W.178 Ligands: NDP.3 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:W.177, B:W.178, A:F.215 4IS.6: 11 residues within 4Å: Chain C: V.120, T.121, C.122, Y.170, M.174, W.177, W.178 Chain D: F.215, D.233, M.237 Ligands: NAP.5 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.215, D:D.233, C:W.177, C:W.178 4IS.7: 12 residues within 4Å: Chain C: F.215, Y.219, D.233, M.237, F.279 Chain D: C.122, P.123, Y.170, M.174, W.177, W.178 Ligands: NDP.8 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:W.177, D:W.178 Halogen bonds: D:Y.170, C:Y.219

1 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.5: 25 residues within 4Å: Chain C: G.11, L.12, G.13, P.14, M.15, N.34, R.35, T.36, R.39, S.67, L.68, T.69, A.73, L.77, L.93, S.94, S.95, V.120, C.122, P.124, Y.170 Chain D: A.232, R.234, M.237 Ligands: 4IS.6 18 PLIP interactions: 16 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:L.12, C:M.15, C:N.34, C:N.34, C:R.35, C:T.36, C:T.36, C:L.68, C:T.69, C:S.95, D:A.232 Water bridges: C:G.13, C:G.16 Salt bridges: C:R.35, C:R.39, D:R.234 pi-Cation interactions: C:R.35, C:R.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, Q. et al., Engineered Imine Reductase for Larotrectinib Intermediate Manufacture. Acs Catalysis (2022)

Release Date

2023-06-28

Peptides

reductase for protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

reductase for protein

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