SMTL ID : 5m0m.1

Structure-based evolution of a hybrid steroid series of Autotaxin inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]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-MAN-MAN-MAN.1: 19 residues within 4Å: Chain A: L.185, Y.186, E.188, S.189, H.190, G.191, G.220, G.221, Q.222, K.230, H.398, N.401, N.402, P.487, N.488, N.489, D.708, L.710, H.796 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.185

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

IOD.2: 3 residues within 4Å: Chain A: G.194, N.195, R.356 Ligand excluded by PLIP IOD.3: 3 residues within 4Å: Chain A: S.601, A.746, D.747 Ligand excluded by PLIP IOD.4: 2 residues within 4Å: Chain A: L.753, E.812 Ligand excluded by PLIP IOD.5: 4 residues within 4Å: Chain A: H.246, S.272, I.296, T.299 Ligand excluded by PLIP IOD.6: 1 residues within 4Å: Chain A: N.364 Ligand excluded by PLIP IOD.7: 2 residues within 4Å: Chain A: P.422, L.423 Ligand excluded by PLIP IOD.8: 3 residues within 4Å: Chain A: M.197, Y.198, R.358 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: F.527, L.529, C.531 Ligand excluded by PLIP IOD.10: 1 residues within 4Å: Chain A: S.811 Ligand excluded by PLIP IOD.11: 3 residues within 4Å: Chain A: R.711, T.713, E.714 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain A: T.237, A.269 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain A: H.162, P.164, K.464 Ligand excluded by PLIP

2 x ZN: ZINC ION(Non-covalent)

ZN.14: 3 residues within 4Å: Chain A: D.276, H.280, H.439 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.276, A:D.276, A:H.280, A:H.439, H2O.4 ZN.15: 4 residues within 4Å: Chain A: D.136, T.174, D.323, H.324 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.136, A:D.136, A:T.174, A:D.323, A:H.324

1 x CA: CALCIUM ION(Non-covalent)

CA.16: 5 residues within 4Å: Chain A: D.704, N.706, D.708, L.710, D.712 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.704, A:D.708, A:L.710, A:D.712, H2O.1

1 x 7CF: [3,5-bis(chloranyl)phenyl]methyl (3~{R})-3-[[(4~{R})-4-[(3~{R},5~{S},7~{S},8~{R},9~{S},10~{S},13~{R},14~{S},17~{R})-10,13-dimethyl-3,7-bis(oxidanyl)-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthren-17-yl]pentanoyl]amino]pyrrolidine-1-carboxylate(Non-covalent)

7CF.17: 18 residues within 4Å: Chain A: L.43, Y.47, I.132, S.134, F.175, L.178, L.208, K.213, F.214, W.219, P.223, W.225, F.238, F.239, W.240, V.242, Y.271 Ligands: NKP.37 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.43, A:F.175, A:L.178, A:K.213, A:F.214, A:W.219, A:W.219, A:F.238, A:F.239, A:F.239, A:F.239, A:Y.271 Hydrogen bonds: A:W.225, A:W.240 pi-Stacking: A:F.238

2 x NA: SODIUM ION(Non-functional Binders)

NA.18: 4 residues within 4Å: Chain A: Y.634, D.637, K.638, M.640 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.640 NA.19: 4 residues within 4Å: Chain A: N.766, D.767, S.769, S.772 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.766

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

SCN.20: 4 residues within 4Å: Chain A: K.45, S.48, S.49, C.50 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.45 SCN.21: 3 residues within 4Å: Chain A: F.644, W.677, Q.681 No protein-ligand interaction detected (PLIP) SCN.22: 2 residues within 4Å: Chain A: L.341, N.343 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.343 SCN.23: 4 residues within 4Å: Chain A: V.149, R.294, D.297, K.298 No protein-ligand interaction detected (PLIP) SCN.24: 3 residues within 4Å: Chain A: K.460, Y.461, R.500 No protein-ligand interaction detected (PLIP) SCN.25: 3 residues within 4Å: Chain A: R.514, N.516, S.573 No protein-ligand interaction detected (PLIP) SCN.33: 8 residues within 4Å: Chain A: V.169, Y.170, Y.186, P.187, E.188, L.397, H.398, Y.399 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.188 SCN.34: 7 residues within 4Å: Chain A: F.590, I.702, F.703, R.711, D.712, L.797 Ligands: GOL.27 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.703 SCN.35: 8 residues within 4Å: Chain A: P.467, F.468, E.472, S.494, L.495, H.497, T.815, T.818 No protein-ligand interaction detected (PLIP) SCN.36: 8 residues within 4Å: Chain A: L.376, T.377, C.378, Q.383, F.385, K.386, P.387, C.770 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.378, A:Q.383, A:K.386

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.26: 4 residues within 4Å: Chain A: P.671, A.672, R.675, N.766 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.675, A:N.766, A:N.766 Water bridges: A:S.772, A:S.772 GOL.27: 8 residues within 4Å: Chain A: Y.570, L.594, P.701, F.703, R.711, Y.733, T.798 Ligands: SCN.34 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.570, A:L.594, A:P.701 GOL.28: 1 residues within 4Å: Chain A: C.331 No protein-ligand interaction detected (PLIP) GOL.29: 3 residues within 4Å: Chain A: K.421, P.422, L.423 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.423 GOL.30: 4 residues within 4Å: Chain A: I.347, T.348, L.349, R.420 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.349, A:R.420 GOL.31: 11 residues within 4Å: Chain A: N.475, V.476, D.479, T.491, H.492, G.493, S.494, L.495, N.496, L.499, N.502 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.479, A:G.493, A:S.494, A:L.495, A:L.495 Water bridges: A:E.472 GOL.32: 5 residues within 4Å: Chain A: P.164, K.464, V.465, P.466, P.467 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.464

1 x NKP: (2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate(Non-covalent)

NKP.37: 10 residues within 4Å: Chain A: P.35, S.46, S.48, L.208, R.209, G.210, R.211, K.213, F.214 Ligands: 7CF.17 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.35, A:R.211, A:F.214 Hydrogen bonds: A:L.208, A:G.210, A:K.213 Salt bridges: A:K.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Keune, W.J. et al., Rational Design of Autotaxin Inhibitors by Structural Evolution of Endogenous Modulators. J. Med. Chem. (2017)

Release Date

2017-08-16

Peptides

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2

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