SMTL ID : 7er9.1

Crystal structure of human Biliverdin IX-beta reductase B with Febuxostat (TEI)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 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.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, H.142, P.161, P.162, H.163, I.164 Ligands: TEI.2 33 PLIP interactions: 33 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 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: TEI.6 35 PLIP interactions: 35 interactions with chain B Hydrophobic interactions: 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:H.163, B:I.164 Water bridges: B:G.20, B:G.20, 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:T.87, B:R.88, B:R.88, B:R.88 Salt bridges: B:R.45, B:R.49, B:R.88, B:R.88 pi-Cation interactions: B:R.45

2 x TEI: 2-(3-CYANO-4-ISOBUTOXY-PHENYL)-4-METHYL-5-THIAZOLE-CARBOXYLIC ACID(Non-covalent)

TEI.2: 12 residues within 4Å: Chain A: L.91, S.121, A.122, F.123, W.126, L.135, H.142, P.162, H.163, R.184, Y.210 Ligands: NAP.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.91, A:F.123, A:F.123, A:L.135, A:L.135, A:R.184 Hydrogen bonds: A:S.121, A:H.142, A:H.163 TEI.6: 14 residues within 4Å: Chain A: D.140 Chain B: R.88, S.121, A.122, F.123, W.126, L.135, V.138, H.142, P.162, H.163, R.180, R.184 Ligands: NAP.5 9 PLIP interactions: 1 interactions with chain A, 8 interactions with chain B Water bridges: A:R.144, B:S.121 Hydrophobic interactions: B:R.88, B:F.123, B:L.135 Hydrogen bonds: B:A.122 Salt bridges: B:R.180, B:R.184 pi-Stacking: B:F.123

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

SO4.3: 1 residues within 4Å: Chain A: H.193 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.171, A:H.193 Salt bridges: A:H.193 SO4.4: 3 residues within 4Å: Chain A: S.183, R.184, V.185 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.182, A:R.184, A:V.185 Salt bridges: A:R.184 SO4.7: 7 residues within 4Å: Chain A: K.147, R.150 Chain B: H.163, G.165, D.166, Q.167, V.185 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Water bridges: A:K.147 Salt bridges: A:R.150, B:H.163 Hydrogen bonds: B:D.166, B:Q.167, B:Q.167 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, B:Y.38

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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