SMTL ID : 5m0s.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: 17 residues within 4Å: Chain A: L.185, Y.186, E.188, S.189, H.190, G.220, G.221, Q.222, K.230, H.398, N.401, N.402, P.487, N.488, N.489, L.710, H.796 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.185

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.704, N.706, D.708, L.710, D.712, E.716 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

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 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.3 ZN.4: 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

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

IOD.5: 4 residues within 4Å: Chain A: G.194, N.195, S.196, R.356 Ligand excluded by PLIP IOD.6: 3 residues within 4Å: Chain A: S.601, A.746, D.747 Ligand excluded by PLIP IOD.7: 2 residues within 4Å: Chain A: L.529, C.531 Ligand excluded by PLIP IOD.8: 3 residues within 4Å: Chain A: H.246, S.272, T.299 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: M.197, Y.198 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: L.753, R.808 Ligand excluded by PLIP IOD.11: 1 residues within 4Å: Chain A: P.128 Ligand excluded by PLIP IOD.12: 1 residues within 4Å: Chain A: C.50 Ligand excluded by PLIP IOD.13: 3 residues within 4Å: Chain A: R.711, T.713, E.714 Ligand excluded by PLIP IOD.14: 1 residues within 4Å: Chain A: S.811 Ligand excluded by PLIP IOD.15: 3 residues within 4Å: Chain A: G.352, H.417, V.418 Ligand excluded by PLIP IOD.16: 2 residues within 4Å: Chain A: N.363, N.364 Ligand excluded by PLIP IOD.35: 2 residues within 4Å: Chain A: K.464, P.466 Ligand excluded by PLIP

1 x 7CW: [3,5-bis(chloranyl)phenyl]methyl ~{N}-[2-[[(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]ethyl]carbamate(Non-covalent)

7CW.17: 16 residues within 4Å: Chain A: L.43, Y.47, I.132, S.134, F.175, L.178, A.182, K.213, F.214, H.216, W.219, W.225, F.238, F.239, W.240, Y.271 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.175, A:L.178, A:K.213, A:F.214, A:F.214, A:W.219, A:W.219, A:F.239, A:F.239 Hydrogen bonds: A:W.225, A:W.240, A:W.240

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

NA.18: 3 residues within 4Å: Chain A: Y.634, D.637, M.640 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.640

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

SCN.19: 3 residues within 4Å: Chain A: S.641, P.671, K.674 No protein-ligand interaction detected (PLIP) SCN.20: 3 residues within 4Å: Chain A: K.460, Y.461, R.500 No protein-ligand interaction detected (PLIP) SCN.21: 4 residues within 4Å: Chain A: S.141, Y.142, K.145, F.285 No protein-ligand interaction detected (PLIP) SCN.22: 3 residues within 4Å: Chain A: T.572, S.573, I.589 No protein-ligand interaction detected (PLIP) SCN.23: 3 residues within 4Å: Chain A: T.229, G.232, R.234 No protein-ligand interaction detected (PLIP) SCN.24: 5 residues within 4Å: Chain A: F.125, V.126, D.261, R.264, S.266 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.127 SCN.25: 5 residues within 4Å: Chain A: L.349, P.351, A.419, R.420, D.424 No protein-ligand interaction detected (PLIP) SCN.26: 5 residues within 4Å: Chain A: N.475, P.487, N.488, G.490, H.492 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.475, A:N.488, A:H.492 SCN.27: 3 residues within 4Å: Chain A: L.341, T.342, T.371 No protein-ligand interaction detected (PLIP) SCN.28: 6 residues within 4Å: Chain A: F.468, E.472, S.494, L.495, T.815, T.818 No protein-ligand interaction detected (PLIP) SCN.29: 3 residues within 4Å: Chain A: S.754, V.755, Y.819 No protein-ligand interaction detected (PLIP)

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.30: 1 residues within 4Å: Chain A: V.75 No protein-ligand interaction detected (PLIP) GOL.31: 6 residues within 4Å: Chain A: Q.391, H.392, D.704, Y.707, T.730, H.731 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.392, A:D.704, A:R.763 GOL.32: 4 residues within 4Å: Chain A: T.507, P.509, R.792, Y.810 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.792, A:Y.810 GOL.33: 7 residues within 4Å: Chain A: Y.570, F.590, L.594, P.701, F.703, R.711, T.798 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.570, A:P.701, A:R.711 Water bridges: A:D.712 GOL.34: 2 residues within 4Å: Chain A: D.765, D.767 No protein-ligand interaction detected (PLIP)

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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