SMTL ID : 8w30.1

Crystal structure of alpha-V beta-1 integrin headpiece in complex with TR01225179

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

hetero-1-1-mer

Ligands

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.1: 7 residues within 4Å: Chain A: E.15, G.16, S.17, K.42, N.44, V.51, E.52 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-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-MAN-MAN-MAN.2: 7 residues within 4Å: Chain A: A.213, Q.214, F.217, Y.254, S.263, L.264, N.266 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.214, A:Q.214 Hydrophobic interactions: A:F.217

6 x CA: CALCIUM ION(Non-covalent)

CA.3: 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 CA.4: 5 residues within 4Å: Chain A: D.284, N.286, D.288, Y.290, D.292 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.284, A:D.288, A:Y.290, A:D.292, H2O.1 CA.5: 6 residues within 4Å: Chain A: D.349, D.351, D.353, F.355, D.357, N.377 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 CA.6: 5 residues within 4Å: Chain A: D.413, D.415, N.417, Y.419, D.421 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.415, A:D.415, A:Y.419, A:D.421, H2O.1 CA.10: 6 residues within 4Å: Chain B: D.130, S.132, S.134, E.229, D.259 Ligands: 01.14 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:S.132, B:S.134, B:E.229 CA.11: 6 residues within 4Å: Chain B: E.169, N.224, D.226, S.227, P.228, E.229 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.169, B:D.226, B:D.226, B:P.228, B:E.229

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

NAG.7: 2 residues within 4Å: Chain A: N.260, S.262 No protein-ligand interaction detected (PLIP) NAG.8: 4 residues within 4Å: Chain A: P.451, N.458, T.460, C.472 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.458, A:T.460 NAG.9: 4 residues within 4Å: Chain A: N.492, Q.494, N.524, Y.565 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.492, A:N.524, A:Y.565 NAG.12: 2 residues within 4Å: Chain B: G.384, N.386 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.384, B:N.386 NAG.13: 3 residues within 4Å: Chain B: W.247, N.249, T.431 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.249

1 x 01: N-(2,4-dichlorobenzoyl)-L-phenylalanine

01.14: 14 residues within 4Å: Chain A: Y.178 Chain B: S.132, Y.133, S.134, K.182, P.186, C.187, G.223, N.224, L.225, D.226, S.227, E.229 Ligands: CA.10 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.225, A:Y.178 Hydrogen bonds: B:Y.133, B:S.134, B:N.224, B:N.224, B:N.224

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sabat, M. et al., Design and Discovery of a Potent and Selective Inhibitor of Integrin alpha v beta 1. J.Med.Chem. (2024)

Release Date

2025-01-01

Peptides

Integrin alpha-V heavy chain: A
Integrin beta-1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Integrin alpha-V heavy chain

Integrin beta-1