SMTL ID : 7er8.1

Crystal structure of human Biliverdin IX-beta reductase B with Sulfasalazine (SAS)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

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

NAP.1: 27 residues within 4Å: Chain A: G.20, A.21, T.22, G.23, Q.24, T.25, R.45, S.48, D.64, V.65, L.84, L.85, G.86, T.87, R.88, V.96, M.97, C.119, T.120, S.121, V.138, H.142, P.161, P.162, H.163, I.164 Ligands: SAS.2 37 PLIP interactions: 37 interactions with chain A Hydrophobic interactions: A:P.161, A:I.164, A:I.164 Hydrogen bonds: A:G.20, A:T.22, A:T.22, A:Q.24, A:Q.24, A:T.25, A:R.45, A:S.48, A:D.64, A:V.65, A:L.85, A:G.86, A:R.88, A:H.163, A:I.164 Water bridges: A:G.20, A:A.21, A:T.22, A:G.23, A:G.26, A:R.45, A:R.45, A:R.45, A:R.45, A:T.87, A:T.87, A:T.87, A:R.88, A:R.88, A:I.164 Salt bridges: A:R.45, A:R.88, A:R.88 pi-Cation interactions: A:R.45 NAP.5: 25 residues within 4Å: Chain B: G.20, A.21, T.22, G.23, Q.24, T.25, R.45, R.49, D.64, V.65, L.84, L.85, G.86, R.88, V.96, M.97, C.119, T.120, S.121, H.142, P.161, P.162, H.163, I.164 Ligands: SAS.6 36 PLIP interactions: 36 interactions with chain B Hydrophobic interactions: B:P.161, B:I.164, B:I.164 Hydrogen bonds: B:G.20, B:T.22, B:T.22, B:T.22, B:G.23, B:Q.24, B:Q.24, B:T.25, B:T.25, B:D.64, B:V.65, B:L.85, B:G.86, B:R.88, B:I.164 Water bridges: B:G.20, B:A.21, B:G.26, B:R.45, B:R.45, B:R.45, B:R.45, B:R.45, B:T.87, B:T.87, B:R.88, B:R.88, B:H.163 Salt bridges: B:R.45, B:R.49, B:R.88, B:R.88 pi-Cation interactions: B:R.45

2 x SAS: 2-HYDROXY-(5-([4-(2-PYRIDINYLAMINO)SULFONYL]PHENYL)AZO)BENZOIC ACID(Non-covalent)

SAS.2: 14 residues within 4Å: Chain A: L.91, S.121, A.122, F.123, W.126, L.135, V.138, P.162, H.163, R.180, G.181, R.184, Y.210 Ligands: NAP.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:A.122, A:W.126, A:L.135, A:L.135, A:V.138, A:R.184 Hydrogen bonds: A:W.126, A:H.163, A:R.180 Water bridges: A:T.87, A:R.134, A:R.184 pi-Stacking: A:F.123 pi-Cation interactions: A:R.180 SAS.6: 16 residues within 4Å: Chain A: E.99, D.140, R.144 Chain B: T.87, R.88, N.89, D.90, L.91, S.121, F.123, W.126, R.134, L.135, P.162, H.163 Ligands: NAP.5 16 PLIP interactions: 4 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:E.99, B:F.123, B:F.123, B:R.134, B:L.135 Water bridges: A:R.144, A:R.144, B:T.87, B:D.90 Salt bridges: A:R.144, B:H.163 Hydrogen bonds: B:N.89, B:N.89, B:D.90, B:H.163, B:R.184

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

SO4.3: 3 residues within 4Å: Chain A: H.146, R.150, S.208 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.208, A:S.208 Salt bridges: A:H.146, A:R.150 SO4.4: 1 residues within 4Å: Chain A: H.193 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.193 SO4.7: 7 residues within 4Å: Chain A: K.147, R.150 Chain B: H.163, G.165, D.166, Q.167, V.185 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.166, B:Q.167, B:Q.167 Salt bridges: B:H.163, A:R.150 Water bridges: A:K.147, A:R.150 SO4.8: 4 residues within 4Å: Chain B: V.13, A.36, G.37, Y.38 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.36 Water bridges: B:Y.38 SO4.9: 2 residues within 4Å: Chain B: K.188, H.189 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.188 Salt bridges: B:K.188, B:H.189

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, M. et al., Repositioning Food and Drug Administration-Approved Drugs for Inhibiting Biliverdin IX beta Reductase B as a Novel Thrombocytopenia Therapeutic Target. J.Med.Chem. (2022)

Release Date

2022-01-19

Peptides

Flavin reductase (NADPH): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Flavin reductase (NADPH)

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