SMTL ID : 9cz7.1

Crystal structure of integrin avb6 headpiece in complex with compound 12

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.57 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

2 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: Y.450, P.451, N.458, T.460, C.461, C.472, F.473 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 10 residues within 4Å: Chain A: P.14, E.15, G.16, S.17, K.42, A.43, N.44, V.51, E.52, H.91 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-(1-6)-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.3: 7 residues within 4Å: Chain A: N.232, G.233, D.234, D.257, K.259, N.260, S.262 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.233

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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.4: 10 residues within 4Å: Chain A: A.213, Q.214, F.217, M.252, Y.254, S.263, L.264, Y.265, N.266 Ligands: GOL.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.214, A:Q.214 Hydrophobic interactions: A:A.213, A:F.217

6 x CA: CALCIUM ION(Non-covalent)

CA.5: 6 residues within 4Å: Chain A: D.230, F.231, N.232, D.234, I.236, D.238 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.230, A:D.234, A:I.236, A:D.238, H2O.1 CA.6: 8 residues within 4Å: Chain A: D.349, L.350, D.351, D.353, F.355, D.357, N.377, G.378 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.351, A:D.353, A:F.355, A:D.357, H2O.1 CA.7: 7 residues within 4Å: Chain A: D.413, I.414, D.415, N.417, Y.419, D.421, A.437 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 CA.8: 6 residues within 4Å: Chain A: D.284, I.285, 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.14: 6 residues within 4Å: Chain B: E.158, N.214, D.216, T.217, P.218, E.219 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:E.158, B:D.216, B:D.216, B:P.218, B:E.219 CA.15: 6 residues within 4Å: Chain B: S.123, M.124, D.126, D.127, K.334, D.335 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.123, B:D.126, B:D.127, H2O.2, H2O.2

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 11 residues within 4Å: Chain A: A.140, P.141, S.144, S.201, I.202, K.203, Y.204, Q.207 Chain D: T.28, S.31, F.32 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:I.202, A:Q.207, A:Q.207, D:T.28 GOL.10: 9 residues within 4Å: Chain A: F.21, W.93, A.96, P.110, L.111, F.159 Chain B: K.260, L.261, G.263 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:F.159, B:K.260, B:L.261, B:G.263 GOL.11: 6 residues within 4Å: Chain A: R.211, T.212, A.213 Ligands: NAG-NAG-BMA-MAN-MAN.4, NAG-NAG-BMA-MAN-MAN.4, NAG-NAG-BMA-MAN-MAN.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.211 GOL.12: 8 residues within 4Å: Chain A: F.337, R.339, Y.364, K.369 Chain B: P.267, N.268, D.269, Q.293 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.339, A:R.339, B:Q.293 GOL.18: 8 residues within 4Å: Chain B: A.321, K.322, I.324, P.325, G.326, A.327, E.355, K.384 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.322, B:G.326, B:A.327, B:K.384 GOL.19: 7 residues within 4Å: Chain B: V.61, I.63, P.85, L.88, T.99, L.100, Q.101 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.101, B:Q.101 GOL.22: 10 residues within 4Å: Chain A: Y.80, E.117, M.118 Chain C: Y.32, G.91, N.92, Y.96 Chain D: F.99, R.102, G.103 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:N.92, C:Y.96, A:Y.80, A:Y.80 GOL.23: 6 residues within 4Å: Chain C: G.42 Chain D: V.93, Y.95, Q.110, G.111, S.113 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.95, D:S.113

1 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 6 residues within 4Å: Chain B: S.121, S.123, N.214, E.219, A.251 Ligands: 01.16 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:S.121, B:E.219, H2O.2, H2O.2, H2O.2

1 x 01: (2S)-phenyl{(3S)-3-[4-(5,6,7,8-tetrahydro-1,8-naphthyridin-2-yl)butoxy]pyrrolidin-1-yl}acetic acid

01.16: 19 residues within 4Å: Chain A: D.150, F.177, Y.178, Q.180, T.212, A.213, A.215, D.218 Chain B: S.121, A.122, S.123, I.179, A.213, N.214, I.215, D.216, T.217, E.219 Ligands: MG.13 11 PLIP interactions: 5 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:Y.178, A:Y.178, A:T.212, B:A.122 Hydrogen bonds: A:Q.180, A:D.218, B:S.121, B:A.122, B:N.214, B:N.214, B:N.214

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

NAG.17: 3 residues within 4Å: Chain B: N.76, S.78, D.79 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.76, B:D.79 NAG.21: 1 residues within 4Å: Chain B: N.239 No protein-ligand interaction detected (PLIP)

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

ACT.20: 8 residues within 4Å: Chain B: R.73, E.108, D.109, S.143, K.144, L.145, T.146, S.147 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.143 ACT.24: 7 residues within 4Å: Chain A: V.199, I.202, K.203 Chain C: H.55 Chain D: L.100, D.106, Y.107 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:L.100, D:D.106, D:Y.107 Hydrogen bonds: D:Y.107, D:Y.107, A:K.203 Water bridges: A:K.203

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Harrison, B.A. et al., The Discovery of MORF-627, a Highly Selective Conformationally-Biased Zwitterionic Integrin alpha v beta 6 Inhibitor for Fibrosis. J.Med.Chem. (2024)

Release Date

2024-11-13

Peptides

Integrin alpha-V heavy chain: A
Integrin beta-6: B
17E6 Fab light chain: C
17E6 Fab heavy chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Integrin alpha-V heavy chain

Integrin beta-6

17E6 Fab light chain

17E6 Fab heavy chain

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