SMTL ID : 8r5l.1

E-selectin complexed with glycomimetic ligand BW850

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

7 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 3 residues within 4Å: Chain A: L.176, Y.181, N.182 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.176 Hydrogen bonds: A:N.182 NAG.2: 3 residues within 4Å: Chain A: N.139, Y.140, K.152 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.151 Water bridges: A:N.138 NAG.3: 4 residues within 4Å: Chain A: Q.155, I.156, N.158 Ligands: NAG.4 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.155 Hydrogen bonds: A:Q.155, A:I.156 NAG.4: 2 residues within 4Å: Chain A: N.178 Ligands: NAG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.178 NAG.5: 2 residues within 4Å: Chain A: N.4, R.22 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.18 Water bridges: A:Y.18, A:R.22 NAG.6: 1 residues within 4Å: Chain A: N.124 No protein-ligand interaction detected (PLIP) NAG.7: 4 residues within 4Å: Chain A: Y.193, V.218, W.243, N.244 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.218, A:W.243 Hydrogen bonds: A:N.244

1 x CA: CALCIUM ION(Non-covalent)

CA.8: 6 residues within 4Å: Chain A: E.80, N.82, E.88, N.105, D.106 Ligands: Y6T.9 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.80, A:E.88, A:D.106, A:D.106

1 x Y6T: (2~{S})-3-cyclohexyl-2-[(2~{R},3~{R},4~{S},5~{S},6~{R})-2-[(1~{R},2~{R},3~{S},5~{R})-3-ethyl-2-[(2~{S},3~{S},4~{R},5~{S},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-[3-[1-[3-oxidanylidene-3-[(3,6,8-trisulfonaphthalen-1-yl)amino]propyl]-1,2,3-triazol-4-yl]propylcarbamoyl]cyclohexyl]oxy-6-(hydroxymethyl)-5-oxidanyl-3-(phenylcarbonyloxy)oxan-4-yl]oxy-propanoic acid(Non-covalent)

Y6T.9: 18 residues within 4Å: Chain A: Y.48, E.80, N.82, R.84, Q.85, D.87, E.88, E.92, Y.94, R.97, E.98, N.105, D.106, E.107, R.108, S.110, K.113 Ligands: CA.8 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:R.84 Hydrogen bonds: A:Y.44, A:N.82, A:N.82, A:Q.85, A:D.87, A:E.88, A:E.92, A:R.97, A:N.105, A:N.105, A:S.110, A:S.110 Salt bridges: A:R.84, A:R.97, A:R.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wagner, B. et al., Analogues of the pan-selectin antagonist rivipansel (GMI-1070). Eur.J.Med.Chem. (2024)

Release Date

2024-10-23

Peptides

E-selectin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E-selectin

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