SMTL ID : 6mk0.1

Integrin AlphaVBeta3 ectodomain bound to antagonist TDI-4161

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.01 Å

Oligo State

hetero-1-1-mer

Ligands

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 6 residues within 4Å: Chain A: E.15, G.16, S.17, K.42, N.44, E.52 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: Y.450, P.451, N.458, C.472 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: P.819, N.821, Q.885, V.886, G.887 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: N.368, S.395 Ligands: NAG.17 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- BMA- MAN- MAN: alpha-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA-MAN-MAN.2: 8 residues within 4Å: Chain A: A.213, Q.214, F.217, M.252, Y.254, S.263, L.264, N.266 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.214

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.6: 6 residues within 4Å: Chain A: P.624, I.654 Chain B: Y.528, Y.554, N.556, C.580 No protein-ligand interaction detected (PLIP)

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

NAG.7: 3 residues within 4Å: Chain A: D.257, N.260, S.262 No protein-ligand interaction detected (PLIP) NAG.8: 5 residues within 4Å: Chain A: K.501, F.558, P.583, N.585 Chain B: D.509 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.501 NAG.9: 2 residues within 4Å: Chain A: N.804, N.805 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.805 NAG.10: 2 residues within 4Å: Chain A: T.942, N.943 No protein-ligand interaction detected (PLIP) NAG.11: 5 residues within 4Å: Chain A: D.751, H.752, S.919, T.948, N.950 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.919, A:N.950 NAG.17: 2 residues within 4Å: Chain B: N.96 Ligands: NAG-NAG.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.395, B:S.395 NAG.18: 6 residues within 4Å: Chain A: R.248, M.272 Chain B: N.313, L.314, N.317, E.320 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:N.313 Hydrogen bonds: A:R.248 NAG.22: 5 residues within 4Å: Chain B: L.642, D.644, A.649, N.651, Q.665 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:A.649 Hydrogen bonds: B:D.644, B:Q.665

8 x MN: MANGANESE (II) ION(Non-covalent)

MN.12: 5 residues within 4Å: Chain A: D.230, N.232, D.234, I.236, D.238 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.230, A:D.234, A:I.236, A:D.238, A:D.238 MN.13: 5 residues within 4Å: Chain A: D.284, N.286, D.288, Y.290, D.292 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.284, A:D.288, A:Y.290, A:D.292, A:D.292 MN.14: 5 residues within 4Å: Chain A: D.349, D.351, D.353, F.355, D.357 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.349, A:D.351, A:D.353, A:F.355, A:D.357 MN.15: 5 residues within 4Å: Chain A: D.413, D.415, N.417, Y.419, D.421 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.413, A:D.415, A:Y.419, A:D.421, A:D.421 MN.16: 5 residues within 4Å: Chain A: C.596, G.597, D.599, V.601, E.636 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:C.596, A:D.599, A:D.599, A:E.636, A:E.636 MN.19: 3 residues within 4Å: Chain B: S.118, E.217 Ligands: JUY.23 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.118, B:E.217, H2O.1, H2O.1, H2O.1 MN.20: 5 residues within 4Å: Chain B: S.120, M.121, D.123, D.124, M.332 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:S.120, B:D.123, B:D.124, B:M.332, H2O.1 MN.21: 5 residues within 4Å: Chain B: D.155, N.212, D.214, P.216, E.217 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.155, B:D.214, B:D.214, B:P.216, B:E.217

1 x JUY: (2S)-2-[(1,3-benzothiazole-2-carbonyl)amino]-4-{[5-(1,8-naphthyridin-2-yl)pentanoyl]amino}butanoic acid(Non-covalent)

JUY.23: 17 residues within 4Å: Chain A: D.150, F.177, Y.178, Q.180, T.212, A.213, A.215, D.218 Chain B: S.118, Y.119, M.177, R.211, N.212, R.213, A.215, E.217 Ligands: MN.19 15 PLIP interactions: 10 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:M.177, B:A.215, A:D.150, A:Y.178, A:Y.178, A:Y.178 Hydrogen bonds: B:S.118, B:Y.119, B:N.212, B:R.213, A:Q.180 Water bridges: B:S.120, B:S.120, B:A.215 pi-Stacking: B:Y.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, J. et al., Novel Pure alphaVbeta3 Integrin Antagonists That Do Not Induce Receptor Extension, Prime the Receptor, or Enhance Angiogenesis at Low Concentrations. Acs Pharmacol Transl Sci (2019)

Release Date

2019-09-25

Peptides

Integrin alpha-V: A
Integrin beta-3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Integrin alpha-V

Integrin beta-3

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