SMTL ID : 7er7.1

Crystal structure of hyman Biliverdin IX-beta reductase B with Tamibarotene (A80)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

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

NAP.1: 25 residues within 4Å: Chain A: G.11, T.13, G.14, Q.15, T.16, R.36, R.40, D.55, V.56, L.75, L.76, G.77, T.78, R.79, V.87, M.88, C.110, T.111, S.112, H.133, P.152, P.153, H.154, I.155 Ligands: A80.2 34 PLIP interactions: 34 interactions with chain A Hydrophobic interactions: A:I.155, A:I.155 Hydrogen bonds: A:G.11, A:T.13, A:Q.15, A:Q.15, A:T.16, 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:R.36, A:R.36, A:R.36, A:R.36, A:R.36, A:T.78, A:T.78, A:T.78 Salt bridges: A:R.36, A:R.40, A:R.79, A:R.79 pi-Cation interactions: A:R.36 NAP.4: 25 residues within 4Å: Chain B: G.11, T.13, G.14, Q.15, T.16, V.35, R.36, R.40, D.55, V.56, L.57, L.75, L.76, G.77, R.79, V.87, C.110, T.111, S.112, H.133, P.152, P.153, H.154, I.155 Ligands: SO4.9 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:P.152, B:I.155 Hydrogen bonds: B:G.11, B:T.13, B:T.13, B:T.13, B:G.14, B:Q.15, B:T.16, B:T.16, B:R.36, B:V.56, B:L.76, B:G.77, B:I.155 Water bridges: B:G.11, B:G.11, B:G.11, B:Q.15, B:G.17, B:R.79, B:R.79 Salt bridges: B:R.40 pi-Cation interactions: B:R.79

1 x A80: 4-[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbamoyl]benzoic acid(Non-covalent)

A80.2: 13 residues within 4Å: Chain A: N.80, L.82, A.113, F.114, W.117, L.126, V.129, P.153, H.154, R.171, R.175, Y.201 Ligands: NAP.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.113, A:F.114, A:F.114, A:W.117, A:L.126, A:V.129, A:P.153 Salt bridges: A:R.171

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

SO4.3: 3 residues within 4Å: Chain A: S.174, R.175, V.176 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.175, A:V.176 Water bridges: A:P.173, A:S.174, A:S.174, A:R.175, A:R.175 Salt bridges: A:R.175 SO4.5: 7 residues within 4Å: Chain A: K.138, R.141 Chain B: H.154, G.156, D.157, Q.158, V.176 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Water bridges: A:K.138, A:R.141 Salt bridges: A:R.141, B:H.154 Hydrogen bonds: B:D.157, B:Q.158 SO4.6: 1 residues within 4Å: Chain B: K.138 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:K.138 SO4.7: 1 residues within 4Å: Chain B: K.5 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.5 Salt bridges: B:K.5 SO4.8: 3 residues within 4Å: Chain B: V.4, A.27, Y.29 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.29 Water bridges: B:Y.29 SO4.9: 5 residues within 4Å: Chain A: R.135 Chain B: R.79, P.153, H.154 Ligands: NAP.4 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:P.153 Salt bridges: B:R.79, B:H.154, A:R.135 Water bridges: A:R.135

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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