SMTL ID : 5dby.1

Crystal Structure of Equine Serum Albumin in Complex with Diclofenac and Naproxen Obtained in Displacement Experiment

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

monomer

Ligands

1 x DIF: 2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID(Non-covalent)

DIF.1: 10 residues within 4Å: Chain A: L.393, D.401, N.404, A.405, V.408, R.409, K.540, E.541, K.544 Ligands: ACT.13 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.393, A:N.404, A:K.540, A:K.544, A:K.544, A:K.544 Salt bridges: A:R.409, A:K.540

1 x NPS: (2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid(Non-covalent)

NPS.2: 14 residues within 4Å: Chain A: L.386, N.390, C.391, F.402, L.406, R.409, Y.410, K.413, L.429, C.437, S.448, L.452, F.487, S.488 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.386, A:N.390, A:F.402, A:L.406, A:Y.410, A:L.452, A:L.452 Hydrogen bonds: A:Y.410 Water bridges: A:K.413 Salt bridges: A:R.409, A:K.413 pi-Cation interactions: A:R.409

5 x MLI: MALONATE ION(Non-functional Binders)

MLI.3: 4 residues within 4Å: Chain A: Y.333, R.336, H.337 Ligands: MLI.6 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.336, A:R.336, A:H.337 MLI.4: 3 residues within 4Å: Chain A: G.206, E.207, R.208 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.207, A:R.208 MLI.5: 4 residues within 4Å: Chain A: K.412, A.538, T.539, K.540 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.540 Water bridges: A:E.541, A:E.541 Salt bridges: A:K.412, A:K.540 MLI.6: 5 residues within 4Å: Chain A: A.303, L.304, A.305, R.336 Ligands: MLI.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.304, A:A.305 Salt bridges: A:R.336, A:R.336 MLI.7: 6 residues within 4Å: Chain A: L.190, A.193, T.428, H.451, L.454, A.455 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.193, A:T.428 Hydrogen bonds: A:A.455

1 x SIN: SUCCINIC ACID(Non-covalent)

SIN.8: 10 residues within 4Å: Chain A: Y.149, L.218, F.222, L.237, R.256, I.263, S.286, I.289, A.290 Ligands: ACT.17 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.237, A:L.237, A:I.289, A:A.290 Hydrogen bonds: A:Y.149 Salt bridges: A:K.221, A:R.256

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 2 residues within 4Å: Chain A: R.187, H.287 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.287 ACT.10: 3 residues within 4Å: Chain A: Y.496, K.499, K.533 4 PLIP interactions: 4 interactions with chain A Water bridges: A:T.419, A:T.419 Salt bridges: A:K.499, A:K.533 ACT.11: 5 residues within 4Å: Chain A: F.205, K.350, S.479, L.480, A.481 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.205, A:L.480 Hydrogen bonds: A:L.480, A:A.481 Salt bridges: A:K.350 ACT.12: 4 residues within 4Å: Chain A: S.65, H.67, E.95, P.96 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.96 Hydrogen bonds: A:S.65 Salt bridges: A:H.67 ACT.13: 3 residues within 4Å: Chain A: R.409, K.540 Ligands: DIF.1 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.389, A:R.409, A:K.540 ACT.17: 5 residues within 4Å: Chain A: W.213, R.217, L.237 Ligands: SIN.8, LMR.16 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.213, A:L.237 Salt bridges: A:K.198, A:K.221

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.14: 4 residues within 4Å: Chain A: L.115, R.144, H.145, K.185 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.145 FMT.15: 3 residues within 4Å: Chain A: K.198, S.201, W.213 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.201

1 x LMR: (2S)-2-hydroxybutanedioic acid(Non-covalent)

LMR.16: 5 residues within 4Å: Chain A: K.194, R.217, K.221, E.291 Ligands: ACT.17 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.194, A:R.217, A:K.221 Salt bridges: A:K.194, A:K.194, A:R.217, A:K.221

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sekula, B. et al., Structural Insights into the Competitive Binding of Diclofenac and Naproxen by Equine Serum Albumin. J.Med.Chem. (2016)

Release Date

2015-12-23

Peptides

Serum albumin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Serum albumin

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