SMTL ID : 6w35.1

A new Autotaxin Inhibitor for the Treatment of Idiopathic Pulmonary Fibrosis: A Clinical Candidate Discovered Using DNA-Encoded Chemistry

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.1: 14 residues within 4Å: Chain A: L.168, E.171, S.172, H.173, G.203, G.204, Q.205, N.384, N.385, P.470, N.471, N.472, L.689, H.775 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.204, A:Q.205, A:P.470

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

NAG.2: 3 residues within 4Å: Chain A: L.324, T.325, N.358 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.325, A:T.325, A:N.358 Water bridges: A:N.326

1 x SKV: 2-fluoranyl-~{N}-[(2~{R})-1-[1-(2~{H}-indazol-5-yl)-3-methyl-2,4-bis(oxidanylidene)-1,3,8-triazaspiro[4.5]decan-8-yl]-3-methyl-1-oxidanylidene-butan-2-yl]-5-(trifluoromethyl)benzamide(Non-covalent)

SKV.3: 16 residues within 4Å: Chain A: L.26, S.29, Y.30, I.115, S.117, L.161, Y.162, L.164, A.165, K.196, F.197, H.199, W.202, W.208, F.221, F.222 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.161, A:K.196, A:W.202, A:W.202, A:W.202, A:F.221, A:F.222 Hydrogen bonds: A:S.29, A:S.29 Water bridges: A:F.222 pi-Stacking: A:F.197, A:F.197, A:W.202, A:W.202, A:F.221, A:F.222

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: D.119, T.157, D.306, H.307 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.119, A:D.119, A:T.157, A:D.306, A:H.307 ZN.5: 3 residues within 4Å: Chain A: D.259, H.263, H.422 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.259, A:D.259, A:H.263, A:H.422, H2O.16

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 4 residues within 4Å: Chain A: N.745, E.746, S.748, S.751 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:N.745, A:S.748, A:S.751, H2O.4, H2O.9, H2O.17 CA.7: 5 residues within 4Å: Chain A: D.683, D.685, D.687, L.689, D.691 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.683, A:D.685, A:D.687, A:L.689, A:D.691, H2O.13

2 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 3 residues within 4Å: Chain A: Y.613, D.616, M.619 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.613, A:D.616, A:M.619, H2O.16 MG.9: 3 residues within 4Å: Chain A: T.515, S.594, C.595 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.515, A:T.515, A:S.594, H2O.13, H2O.15, H2O.16

3 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.10: 4 residues within 4Å: Chain A: P.147, K.447, V.448, P.449 No protein-ligand interaction detected (PLIP) SCN.25: 3 residues within 4Å: Chain A: K.443, Y.444, R.483 No protein-ligand interaction detected (PLIP) SCN.26: 4 residues within 4Å: Chain A: K.28, T.31, S.32, C.33 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.28

12 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 1 residues within 4Å: Chain A: R.386 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain A: M.180, Y.181, T.188, V.333, R.341 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain A: D.720 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: D.329, N.347, Y.350 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain A: H.591 Ligand excluded by PLIP CL.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain A: P.650, K.653 Ligand excluded by PLIP CL.22: 1 residues within 4Å: Chain A: M.491 Ligand excluded by PLIP CL.23: 1 residues within 4Å: Chain A: T.551 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain A: D.517, D.518, K.519 Ligand excluded by PLIP CL.28: 4 residues within 4Å: Chain A: T.578, S.580, A.725, D.726 Ligand excluded by PLIP CL.29: 4 residues within 4Å: Chain A: C.104, F.108, R.110, P.111 Ligand excluded by PLIP

5 x IOD: IODIDE ION(Non-functional Binders)

IOD.17: 2 residues within 4Å: Chain A: Q.257, S.261 Ligand excluded by PLIP IOD.18: 2 residues within 4Å: Chain A: L.732, R.787 Ligand excluded by PLIP IOD.19: 2 residues within 4Å: Chain A: K.521, L.522 Ligand excluded by PLIP IOD.20: 2 residues within 4Å: Chain A: L.512, C.514 Ligand excluded by PLIP IOD.27: 3 residues within 4Å: Chain A: G.177, N.178, R.339 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cuozzo, J.W. et al., Novel Autotaxin Inhibitor for the Treatment of Idiopathic Pulmonary Fibrosis: A Clinical Candidate Discovered Using DNA-Encoded Chemistry. J.Med.Chem. (2020)

Release Date

2020-07-08

Peptides

Ectonucleotide pyrophosphatase/phosphodiesterase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ectonucleotide pyrophosphatase/phosphodiesterase 2