SMTL ID : 7ere.1 (1 other biounit)

Crystal structure of human Biliverdin IX-beta reductase B with Pyrantel Pamoate (PPA)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 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.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, H.133, P.152, P.153, H.154, I.155 Ligands: JBR.2 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: 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:T.16, A:S.39, A:D.55, A:V.56, A:L.76, A:G.77, A:R.79, A:I.155 Water bridges: A:G.11, A:A.12, A:G.14, A:G.17, A:R.36, A:R.36, A:R.36, A:R.36, A:T.78, A:T.78, A:T.78, A:R.79, A:H.154 Salt bridges: A:R.36, A:R.79, A:R.79 pi-Cation interactions: A:R.36 NAP.5: 25 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, R.79, V.87, M.88, C.110, T.111, S.112, H.133, P.152, P.153, H.154, I.155 Ligands: JBR.3 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: 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:Q.15, B:G.17, B:R.36, B:R.36, B:R.36, B:T.78, B:R.79, B:R.79 Salt bridges: B:R.36, B:R.40, B:R.79, B:R.79 pi-Cation interactions: B:R.36

2 x JBR: 4-[(3-carboxy-2-oxidanyl-naphthalen-1-yl)methyl]-3-oxidanyl-naphthalene-2-carboxylic acid(Non-covalent)

JBR.2: 13 residues within 4Å: Chain A: S.112, A.113, F.114, W.117, P.123, R.125, P.152, P.153, H.154, R.171, R.175, Y.201 Ligands: NAP.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.117, A:W.117, A:P.123, A:P.153 Hydrogen bonds: A:R.125, A:Y.201 Water bridges: A:R.171 Salt bridges: A:H.154, A:R.171 pi-Stacking: A:F.114 JBR.3: 14 residues within 4Å: Chain A: T.86, S.89, E.90, R.93, R.135, K.138, V.139 Chain B: Q.15, F.114, L.126, V.129, H.133, H.154 Ligands: NAP.5 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.114, B:L.126, B:V.129, A:V.139 Water bridges: B:H.154, A:R.135 Salt bridges: B:H.154, A:R.93, A:R.135 Hydrogen bonds: A:S.89

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

SO4.4: 1 residues within 4Å: Chain A: R.171 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.171 SO4.6: 7 residues within 4Å: Chain A: K.138, R.141 Chain B: H.154, G.156, D.157, Q.158, V.176 8 PLIP interactions: 4 interactions with chain B, 4 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, A:R.141 SO4.7: 3 residues within 4Å: Chain B: A.27, G.28, Y.29 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.29 Water bridges: B:Y.29

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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