SMTL ID : 7qfe.1

Crystal structure of Human Serum albumin in complex with Gemfibrozil

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

2 x MYR: MYRISTIC ACID(Non-covalent)

MYR.1: 11 residues within 4Å: Chain A: L.22, F.70, Y.150, P.152, L.251, A.254, R.257, A.258, L.283, L.284, S.287 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.22, A:F.70, A:P.152, A:L.251, A:L.283, A:L.284 Hydrogen bonds: A:Y.150, A:S.287, A:S.287 Salt bridges: A:R.257 MYR.2: 13 residues within 4Å: Chain A: S.342, V.344, R.348, P.384, I.388, N.391, F.403, L.407, L.430, V.433, M.446, L.453, R.485 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.344, A:P.384, A:I.388, A:N.391, A:F.403, A:L.407, A:V.433, A:L.453 Hydrogen bonds: A:S.342 Salt bridges: A:R.348, A:R.485

2 x 4TX: 5-(2,5-dimethylphenoxy)-2,2-dimethylpentanoic acid(Non-covalent)

4TX.3: 12 residues within 4Å: Chain A: L.387, Y.411, V.415, L.423, V.426, S.427, L.430, L.460, R.485, F.488, S.489, L.491 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.411, A:Y.411, A:Y.411, A:V.415, A:V.426, A:L.460, A:R.485, A:F.488, A:L.491 Hydrogen bonds: A:Y.411, A:Y.411 4TX.12: 13 residues within 4Å: Chain A: K.199, S.202, L.203, A.210, F.211, W.214, R.218, R.222, L.238, H.242, L.481 Ligands: MPD.9, PO4.13 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:K.199, A:F.211, A:W.214, A:L.238, A:L.481 Salt bridges: A:R.222 pi-Stacking: A:F.211

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 3 residues within 4Å: Chain A: R.117, Y.138, Y.161 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.117, A:R.117

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 11 residues within 4Å: Chain A: Y.150, E.153, Q.196, K.199, L.238, V.241, H.242, C.245, R.257 Ligands: MPD.6, MPD.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.257

6 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6: 9 residues within 4Å: Chain A: Y.148, F.149, Y.150, Q.196, C.200, C.245, G.248, L.250 Ligands: PG4.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.250 Hydrogen bonds: A:Y.148, A:F.149, A:Y.150 MPD.7: 8 residues within 4Å: Chain A: R.209, A.213, D.324, L.327, G.328, A.350, K.351, E.354 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.213 Water bridges: A:R.209, A:E.354 MPD.8: 5 residues within 4Å: Chain A: E.17, N.18, L.135, A.158, K.159 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.17, A:L.135, A:A.158 MPD.9: 6 residues within 4Å: Chain A: R.222, S.287, I.290, A.291 Ligands: PG4.5, 4TX.12 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.291 Hydrogen bonds: A:S.287 MPD.10: 8 residues within 4Å: Chain A: I.142, H.146, F.149, Y.161, L.185, R.186, G.189, K.190 No protein-ligand interaction detected (PLIP) MPD.11: 7 residues within 4Å: Chain A: Y.30, H.67, F.70, N.99, D.249, L.250, L.251 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.30, A:F.70, A:L.250, A:L.251 Hydrogen bonds: A:N.99, A:D.249, A:L.250, A:L.251

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.13: 4 residues within 4Å: Chain A: K.199, W.214, S.454 Ligands: 4TX.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.454

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liberi, S. et al., Structural Analysis of Human Serum Albumin in Complex with the Fibrate Drug Gemfibrozil. Int J Mol Sci (2022)

Release Date

2022-03-02

Peptides

Serum albumin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Serum albumin

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