SMTL ID : 7erc.1

Crystal structure of human Biliverdin IX-beta reductase B with Deferasirox (ICL)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

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

NAP.1: 26 residues within 4Å: Chain A: G.10, A.11, T.12, G.13, Q.14, T.15, R.35, S.38, D.54, V.55, L.74, L.75, G.76, T.77, R.78, V.86, M.87, C.109, T.110, S.111, H.132, P.151, P.152, H.153, I.154 Ligands: JBL.2 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:P.151, A:I.154, A:I.154 Hydrogen bonds: A:G.10, A:T.12, A:T.12, A:Q.14, A:Q.14, A:T.15, A:R.35, A:S.38, A:D.54, A:V.55, A:L.75, A:G.76, A:R.78, A:P.152, A:H.153, A:I.154 Water bridges: A:A.11, A:T.12, A:G.13, A:G.16, A:R.35, A:R.35, A:R.35, A:T.77, A:T.77 Salt bridges: A:R.35, A:R.78, A:R.78 pi-Cation interactions: A:R.35 NAP.4: 24 residues within 4Å: Chain B: G.10, A.11, T.12, G.13, Q.14, T.15, R.35, R.39, D.54, V.55, L.74, L.75, G.76, R.78, V.86, M.87, C.109, T.110, S.111, H.132, P.151, P.152, H.153, I.154 32 PLIP interactions: 32 interactions with chain B Hydrophobic interactions: B:P.151, B:I.154, B:I.154 Hydrogen bonds: B:G.10, B:T.12, B:T.12, B:T.12, B:G.13, B:Q.14, B:Q.14, B:T.15, B:T.15, B:D.54, B:V.55, B:L.75, B:G.76, B:I.154 Water bridges: B:A.11, B:G.16, B:R.35, B:R.39, B:R.39, B:R.39, B:R.39, B:T.77, B:T.77, B:R.78 Salt bridges: B:R.35, B:R.39, B:R.78, B:R.78 pi-Cation interactions: B:R.35

1 x JBL: 4-[3,5-bis(2-hydroxyphenyl)-1,2,4-triazol-1-yl]benzoic acid(Non-covalent)

JBL.2: 11 residues within 4Å: Chain A: S.111, A.112, F.113, W.116, L.125, P.152, H.153, R.170, R.174, Y.200 Ligands: NAP.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.112, A:F.113, A:F.113, A:W.116, A:L.125, A:P.152 Hydrogen bonds: A:S.111, A:H.153 Water bridges: A:R.124 Salt bridges: A:R.170 pi-Stacking: A:F.113 pi-Cation interactions: A:R.124

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

SO4.3: 1 residues within 4Å: Chain A: H.183 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.183

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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