SMTL ID : 8k4k.1

Crystal structure of human Biliverdin IX-beta reductase B with Olsalazine carbon derivative

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 1 residues within 4Å: Chain A: H.183 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.183 GOL.2: 3 residues within 4Å: Chain A: A.48, H.49, V.50 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.49, A:V.50 Water bridges: A:V.50 GOL.3: 4 residues within 4Å: Chain A: W.116, D.117, K.120, R.170 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.117, A:K.120 GOL.7: 8 residues within 4Å: Chain A: I.133, K.137, R.140 Chain B: H.153, G.155, D.156, Q.157, V.175 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.140, A:R.140, B:Q.157, B:Q.157 Water bridges: A:H.136

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

SO4.4: 3 residues within 4Å: Chain A: S.173, R.174, V.175 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.174, A:V.175 Water bridges: A:P.172, A:S.173 Salt bridges: A:R.174

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

NAP.5: 27 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, V.128, H.132, P.151, P.152, H.153, I.154 Ligands: VE2.6 34 PLIP interactions: 34 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:S.38, A:D.54, A:V.55, A:L.75, A:G.76, A:R.78, A:R.78, A:H.153, A:I.154 Water bridges: A:G.10, A:A.11, A:T.12, A:G.13, A:G.16, A:R.35, A:R.35, A:R.35, A:R.35, A:T.77, A:T.77, A:T.77 Salt bridges: A:R.35, A:R.78, A:R.78 pi-Cation interactions: A:R.35 NAP.8: 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, V.86, M.87, C.109, T.110, S.111, H.132, P.151, P.152, H.153, I.154 Ligands: VE2.9 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:Q.14, B:Q.14, B:T.15, B:T.15, B:D.54, B:V.55, B:L.75, B:G.76, B:H.153, B:I.154 Water bridges: B:G.10, B:A.11, B:G.13, B:G.16, B:R.35, B:R.35, B:R.35, B:R.35, B:G.76, B:G.76, B:T.77, B:T.77 Salt bridges: B:R.35, B:R.39 pi-Cation interactions: B:R.35

2 x VE2: 5-[(E)-2-(3-carboxy-4-oxidanyl-phenyl)ethenyl]-2-oxidanyl-benzoic acid(Non-covalent)

VE2.6: 8 residues within 4Å: Chain A: A.112, F.113, W.116, L.125, P.152, H.153, R.174 Ligands: NAP.5 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.112, A:F.113, A:F.113, A:F.113, A:W.116, A:L.125, A:P.152 Hydrogen bonds: A:W.116, A:H.153 Water bridges: A:T.77 VE2.9: 12 residues within 4Å: Chain A: D.130, R.134 Chain B: R.78, S.111, F.113, W.116, L.125, V.128, P.152, H.153, R.174 Ligands: NAP.8 15 PLIP interactions: 4 interactions with chain A, 11 interactions with chain B Water bridges: A:D.130, A:R.134, B:T.77, B:T.77 Salt bridges: A:R.92, A:R.134, B:R.78, B:H.153 Hydrophobic interactions: B:F.113, B:W.116, B:L.125, B:L.125, B:V.128 Hydrogen bonds: B:H.153 pi-Stacking: B:F.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jung, H.M. et al., An Innovative Inhibitor with a New Chemical Moiety Aimed at Biliverdin IX beta Reductase for Thrombocytopenia and Resilient against Cellular Degradation. Pharmaceutics (2024)

Release Date

2025-01-22

Peptides

Flavin reductase (NADPH): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Flavin reductase (NADPH)

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