SMTL ID : 5m0e.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

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: 9 residues within 4Å: Chain A: L.185, S.189, H.398, P.487, N.488, N.489, D.708, L.710, H.796 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 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 ZN.3: 4 residues within 4Å: Chain A: D.276, H.280, H.439 Ligands: 7CR.20 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.276, A:D.276, A:H.280, A:H.439

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

IOD.4: 3 residues within 4Å: Chain A: G.194, N.195, R.356 Ligand excluded by PLIP IOD.5: 3 residues within 4Å: Chain A: M.197, Y.198, R.358 Ligand excluded by PLIP IOD.6: 4 residues within 4Å: Chain A: T.599, S.601, A.746, D.747 Ligand excluded by PLIP IOD.7: 4 residues within 4Å: Chain A: F.527, L.529, C.531, P.619 Ligand excluded by PLIP IOD.8: 3 residues within 4Å: Chain A: P.752, L.753, R.808 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain A: N.215, H.216, R.217 Ligand excluded by PLIP IOD.10: 1 residues within 4Å: Chain A: S.811 Ligand excluded by PLIP IOD.11: 2 residues within 4Å: Chain A: R.711, E.714 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain A: T.572, S.573 Ligand excluded by PLIP IOD.13: 1 residues within 4Å: Ligands: GOL.41 Ligand excluded by PLIP IOD.14: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP IOD.15: 2 residues within 4Å: Chain A: T.342, T.371 Ligand excluded by PLIP IOD.43: 1 residues within 4Å: Chain A: R.311 Ligand excluded by PLIP IOD.44: 3 residues within 4Å: Chain A: G.352, H.417, V.418 Ligand excluded by PLIP

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.6

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

NA.17: 4 residues within 4Å: Chain A: N.766, D.767, S.769, S.772 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.766, A:S.772 Water bridges: A:D.767 NA.18: 3 residues within 4Å: Chain A: Y.634, D.637, M.640 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.637, A:M.640

1 x 5JK: 7alpha-hydroxycholesterol(Non-covalent)

5JK.19: 13 residues within 4Å: Chain A: S.46, Y.47, Y.179, K.213, F.214, H.216, W.219, P.223, W.225, I.226, F.239 Ligands: 7CR.20, SCN.21 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.214, A:H.216, A:W.219, A:W.219, A:W.219, A:I.226, A:F.239, A:F.239 Water bridges: A:G.221

1 x 7CR: [3,5-bis(chloranyl)phenyl]methyl 4-[(3~{R})-3-oxidanyl-3-(2-oxidanylidene-3~{H}-1,3-benzoxazol-6-yl)propyl]piperazine-1-carboxylate(Non-covalent)

7CR.20: 20 residues within 4Å: Chain A: I.132, S.134, D.136, T.174, F.175, L.178, A.182, N.195, L.208, R.209, W.225, F.238, F.239, W.240, Y.271, D.276, H.280, H.439 Ligands: ZN.3, 5JK.19 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.208, A:F.239 Hydrogen bonds: A:T.174, A:R.209, A:W.240, A:H.439 Water bridges: A:N.195, A:N.195

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

SCN.21: 6 residues within 4Å: Chain A: W.225, G.236, T.237, F.238, F.239 Ligands: 5JK.19 Ligand excluded by PLIP SCN.22: 6 residues within 4Å: Chain A: H.246, F.270, S.272, E.295, I.296, T.299 Ligand excluded by PLIP SCN.23: 3 residues within 4Å: Chain A: K.45, S.241, S.243 Ligand excluded by PLIP SCN.24: 7 residues within 4Å: Chain A: H.190, G.191, R.217, W.218, G.220, R.404 Ligands: SCN.28 Ligand excluded by PLIP SCN.25: 3 residues within 4Å: Chain A: K.460, Y.461, R.500 Ligand excluded by PLIP SCN.26: 1 residues within 4Å: Chain A: H.216 Ligand excluded by PLIP SCN.27: 2 residues within 4Å: Chain A: L.569, R.711 Ligand excluded by PLIP SCN.28: 4 residues within 4Å: Chain A: N.402, R.403, R.404 Ligands: SCN.24 Ligand excluded by PLIP SCN.29: 3 residues within 4Å: Chain A: K.464, V.465, P.466 Ligand excluded by PLIP SCN.30: 2 residues within 4Å: Chain A: P.671, K.674 Ligand excluded by PLIP SCN.31: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SCN.32: 2 residues within 4Å: Chain A: E.655, Y.658 Ligand excluded by PLIP SCN.33: 3 residues within 4Å: Chain A: E.511, R.565, R.804 Ligand excluded by PLIP SCN.34: 1 residues within 4Å: Chain A: P.36 Ligand excluded by PLIP SCN.35: 3 residues within 4Å: Chain A: L.569, Y.570, R.571 Ligand excluded by PLIP SCN.36: 4 residues within 4Å: Chain A: V.606, S.607, S.608, R.682 Ligand excluded by PLIP SCN.37: 2 residues within 4Å: Chain A: D.510, V.512 Ligand excluded by PLIP

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.38: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.39: 7 residues within 4Å: Chain A: G.643, F.644, Y.649, K.674, W.677, A.678, Q.681 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.644, A:F.644 GOL.40: 3 residues within 4Å: Chain A: K.421, P.422, L.423 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.421, A:L.423 GOL.41: 5 residues within 4Å: Chain A: V.75, R.76, S.85, D.87 Ligands: IOD.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.87, A:D.87 GOL.42: 5 residues within 4Å: Chain A: R.692, C.739, L.740, F.742, S.754 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.740, A:S.754

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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