SMTL ID : 6i6t.1

SEPIAPTERIN REDUCTASE IN COMPLEX WITH COMPOUND 5

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 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.29, A.30, S.31, R.32, G.33, F.34, A.56, R.57, N.58, A.83, D.84, L.85, G.86, N.115, A.116, G.117, L.141, I.170, S.171, S.172, Y.185, K.189, P.213, G.214, P.215, L.216, T.218, M.220, Q.221 Ligands: H5B.2, EDO.4 31 PLIP interactions: 31 interactions with chain A Hydrophobic interactions: A:P.213 Hydrogen bonds: A:S.31, A:S.31, A:S.31, A:R.32, A:R.32, A:F.34, A:R.57, A:N.58, A:D.84, A:D.84, A:L.85, A:G.86, A:N.115, A:G.117, A:Y.185, A:K.189, A:L.216, A:L.216, A:D.219, A:M.220, A:Q.221 Water bridges: A:R.32, A:R.32, A:G.35, A:R.57, A:R.57, A:N.115 Salt bridges: A:R.32, A:R.32, A:R.57 NAP.5: 32 residues within 4Å: Chain B: G.29, A.30, S.31, R.32, G.33, F.34, A.56, R.57, N.58, A.83, D.84, L.85, G.86, N.115, A.116, G.117, L.141, I.170, S.171, S.172, Y.185, K.189, P.213, G.214, P.215, L.216, T.218, D.219, M.220, Q.221 Ligands: H5B.6, EDO.8 33 PLIP interactions: 33 interactions with chain B Hydrophobic interactions: B:P.213 Hydrogen bonds: B:S.31, B:S.31, B:S.31, B:R.32, B:R.32, B:F.34, B:R.57, B:N.58, B:D.84, B:D.84, B:L.85, B:G.86, B:N.115, B:G.117, B:Y.185, B:K.189, B:L.216, B:L.216, B:D.219, B:M.220, B:Q.221 Water bridges: B:R.32, B:G.35, B:R.57, B:R.57, B:R.57, B:N.58, B:N.115, B:D.219 Salt bridges: B:R.32, B:R.32, B:R.57

4 x H5B: 4-bromanyl-1-oxidanyl-naphthalene-2-carboxylic acid(Non-covalent)

H5B.2: 10 residues within 4Å: Chain A: S.172, L.173, C.174, W.182, P.215, L.237, L.240, Y.274 Ligands: NAP.1, EDO.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.173, A:P.215, A:P.215, A:L.237, A:L.240 Hydrogen bonds: A:L.173, A:Q.221 Water bridges: A:G.214 H5B.3: 11 residues within 4Å: Chain A: V.24, C.25, L.26, V.53, L.98, R.99, L.101, P.102, R.103, A.156, F.157 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.24, A:L.26, A:V.53, A:L.98 Salt bridges: A:R.103 pi-Stacking: A:F.157 Halogen bonds: A:P.102 H5B.6: 11 residues within 4Å: Chain B: S.172, L.173, C.174, W.182, P.215, M.233, L.237, L.240, Y.274 Ligands: NAP.5, EDO.8 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.173, B:L.237, B:L.240 Hydrogen bonds: B:L.173 Water bridges: B:G.214 H5B.7: 10 residues within 4Å: Chain B: V.24, C.25, V.53, L.98, R.99, L.101, P.102, R.103, A.156, F.157 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:V.24, B:V.53, B:L.98, B:R.103 Salt bridges: B:R.103 pi-Stacking: B:F.157 Halogen bonds: B:P.102

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 7 residues within 4Å: Chain A: L.119, W.182, Y.185, M.220, Q.221 Ligands: NAP.1, H5B.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.185, A:Q.221 EDO.8: 8 residues within 4Å: Chain B: L.119, W.182, Y.185, M.220, Q.221, A.224 Ligands: NAP.5, H5B.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.185, B:Q.221

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alen, J. et al., Fragment-Based Discovery of Novel Potent Sepiapterin Reductase Inhibitors. J.Med.Chem. (2019)

Release Date

2019-07-10

Peptides

Sepiapterin reductase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Sepiapterin reductase

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