SMTL ID : 7era.1

Crystal structure of human Biliverdin IX-beta reductase B with Olsalazine Sodium (OSS)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 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.11, A.12, T.13, G.14, Q.15, T.16, R.36, S.39, D.55, V.56, L.75, L.76, G.77, T.78, R.79, V.87, M.88, C.110, T.111, S.112, V.129, H.133, P.152, P.153, H.154, I.155 Ligands: JBC.2 36 PLIP interactions: 36 interactions with chain A Hydrophobic interactions: A:P.152, A:I.155, A:I.155 Hydrogen bonds: A:G.11, A:T.13, A:T.13, A:Q.15, A:Q.15, A:T.16, A:R.36, A:S.39, A:D.55, A:V.56, A:L.76, A:G.77, A:R.79, A:H.154, A:I.155 Water bridges: A:G.11, A:A.12, A:T.13, A:G.14, A:G.17, A:R.36, A:R.36, A:S.39, A:T.78, A:T.78, A:T.78, A:R.79, A:R.79, A:I.155 Salt bridges: A:R.36, A:R.79, A:R.79 pi-Cation interactions: A:R.36 NAP.6: 24 residues within 4Å: Chain B: G.11, A.12, T.13, G.14, Q.15, T.16, R.36, R.40, D.55, V.56, L.75, L.76, G.77, V.87, M.88, C.110, T.111, S.112, H.133, P.152, P.153, H.154, I.155 Ligands: JBC.7 33 PLIP interactions: 33 interactions with chain B Hydrophobic interactions: B:P.152, B:I.155, B:I.155 Hydrogen bonds: B:G.11, B:T.13, B:T.13, B:T.13, B:G.14, B:Q.15, B:Q.15, B:T.16, B:T.16, B:D.55, B:V.56, B:L.76, B:G.77, B:I.155 Water bridges: B:G.11, B:A.12, B:G.17, B:R.36, B:R.36, B:R.36, B:R.36, B:R.36, B:R.40, B:R.40, B:T.78, B:T.78, B:T.78 Salt bridges: B:R.36, B:R.40 pi-Cation interactions: B:R.36

2 x JBC: 5-[(E)-(3-carboxy-4-oxidanyl-phenyl)diazenyl]-2-oxidanyl-benzoic acid(Non-covalent)

JBC.2: 12 residues within 4Å: Chain A: R.79, L.82, S.112, A.113, F.114, W.117, L.126, P.152, P.153, H.154, R.175 Ligands: NAP.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.126, A:L.126 Water bridges: A:R.79, A:W.117, A:R.125, A:R.125, A:Y.201 Salt bridges: A:R.175 pi-Stacking: A:F.114 JBC.7: 13 residues within 4Å: Chain A: D.131, R.135 Chain B: R.79, S.112, F.114, W.117, L.126, V.129, H.133, P.153, H.154, R.175 Ligands: NAP.6 17 PLIP interactions: 12 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:W.117, B:L.126, B:L.126, B:V.129 Hydrogen bonds: B:T.78, B:H.154 Water bridges: B:T.78, B:R.175, B:R.175, A:R.93, A:R.93, A:D.131, A:R.135 Salt bridges: B:R.79, B:H.154, A:R.135 pi-Stacking: B:F.114

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

SO4.3: 1 residues within 4Å: Chain A: R.175 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.175 SO4.4: 1 residues within 4Å: Chain A: H.184 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.162, A:H.184 Salt bridges: A:H.184 SO4.5: 3 residues within 4Å: Chain A: A.49, H.50, V.51 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.51 Water bridges: A:A.49, A:H.50 Salt bridges: A:H.50 SO4.8: 7 residues within 4Å: Chain A: K.138, R.141 Chain B: H.154, G.156, D.157, Q.158, V.176 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.157, B:Q.158, B:Q.158 Salt bridges: B:H.154, A:R.141 Water bridges: A:K.138, A:R.141 SO4.9: 4 residues within 4Å: Chain B: V.4, A.27, G.28, Y.29 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:V.4, B:A.27 Water bridges: B:Y.29 SO4.10: 1 residues within 4Å: Chain B: R.135 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.135, B:R.135, B:R.135, B:K.138 Salt bridges: B:K.138

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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