SMTL ID : 6usn.5 (5 other biounits)

Co-crystal structure of SPR with compound 5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.77 Å

Oligo State

homo-dimer

Ligands

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

NAP.1: 31 residues within 4Å: Chain A: G.16, A.17, S.18, R.19, G.20, F.21, A.43, R.44, N.45, A.70, D.71, L.72, N.102, A.103, G.104, L.128, I.157, S.158, S.159, Y.172, K.176, P.200, G.201, P.202, L.203, T.205, D.206, M.207, Q.208 Ligands: GOL.8, QGV.10 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:P.200 Hydrogen bonds: A:S.18, A:S.18, A:R.19, A:R.19, A:F.21, A:R.44, A:N.45, A:D.71, A:D.71, A:L.72, A:G.73, A:N.102, A:G.104, A:K.176, A:L.203, A:L.203, A:T.205, A:D.206, A:M.207, A:Q.208, A:Q.208 Water bridges: A:S.18, A:R.19, A:R.19, A:G.20, A:R.44, A:N.45, A:N.102 Salt bridges: A:R.19, A:R.19, A:R.44 NAP.11: 31 residues within 4Å: Chain B: G.16, A.17, S.18, R.19, G.20, F.21, A.43, R.44, N.45, A.70, D.71, L.72, G.73, N.102, A.103, G.104, L.128, I.157, S.158, S.159, Y.172, K.176, P.200, G.201, P.202, L.203, T.205, D.206, M.207, Q.208 Ligands: QGV.17 31 PLIP interactions: 31 interactions with chain B Hydrophobic interactions: B:P.200 Hydrogen bonds: B:S.18, B:S.18, B:R.19, B:R.19, B:F.21, B:R.44, B:N.45, B:D.71, B:L.72, B:G.73, B:N.102, B:G.104, B:Y.172, B:K.176, B:L.203, B:L.203, B:T.205, B:T.205, B:D.206, B:M.207, B:Q.208, B:Q.208 Water bridges: B:R.19, B:R.19, B:G.20, B:G.22, B:N.102 Salt bridges: B:R.19, B:R.19, B:R.44

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

SO4.2: 1 residues within 4Å: Chain A: R.44 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.44, A:S.105 Salt bridges: A:R.44 SO4.3: 3 residues within 4Å: Chain A: R.194, K.253, S.254 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.194, A:S.254 Water bridges: A:S.254 Salt bridges: A:K.253 SO4.4: 2 residues within 4Å: Chain A: R.50, R.67 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.50, A:R.67 SO4.5: 2 residues within 4Å: Chain A: K.92, G.93 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.93 SO4.12: 1 residues within 4Å: Chain B: R.44 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.19, B:R.44 Salt bridges: B:R.44 SO4.13: 2 residues within 4Å: Chain B: R.221, Q.225 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.225 Salt bridges: B:R.221 SO4.14: 4 residues within 4Å: Chain B: R.194, F.252, K.253, S.254 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:F.252, B:S.254 Salt bridges: B:R.194

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: A.74, E.75, A.76 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.75, A:A.76 GOL.7: 1 residues within 4Å: Chain A: K.237 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.237, A:K.237 GOL.8: 4 residues within 4Å: Chain A: R.19, R.44, N.45 Ligands: NAP.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.19, A:N.45 GOL.15: 3 residues within 4Å: Chain B: A.74, E.75, A.76 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.75, B:A.76

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

PEG.9: 3 residues within 4Å: Chain A: D.219, G.223 Ligands: QGV.10 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.217, A:D.217 PEG.16: 4 residues within 4Å: Chain B: D.219, M.220, G.223 Ligands: QGV.17 No protein-ligand interaction detected (PLIP)

2 x QGV: (2-hydroxyphenyl)[3-methyl-1-(pyridin-2-yl)-1H-pyrazolo[3,4-b]pyridin-5-yl]methanone(Non-covalent)

QGV.10: 12 residues within 4Å: Chain A: S.159, L.160, F.166, W.169, Y.172, P.202, M.207, Q.208, A.211, M.220 Ligands: NAP.1, PEG.9 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.160, A:F.166, A:Y.172, A:A.211 Hydrogen bonds: A:S.159, A:S.159, A:L.160, A:Y.172 pi-Stacking: A:W.169 QGV.17: 11 residues within 4Å: Chain B: S.159, L.160, F.166, W.169, Y.172, P.202, Q.208, A.211, M.220 Ligands: NAP.11, PEG.16 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.166, B:Y.172, B:A.211 Hydrogen bonds: B:S.159, B:S.159, B:L.160 pi-Stacking: B:W.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, H. et al., Virtual screening to identify potent sepiapterin reductase inhibitors. Bioorg.Med.Chem.Lett. (2020)

Release Date

2019-12-11

Peptides

Sepiapterin reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Sepiapterin reductase

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