SMTL ID : 5m0d.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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.1: 15 residues within 4Å: Chain A: L.185, E.188, S.189, H.190, G.220, G.221, Q.222, 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

9 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: M.197, Y.198, R.358 Ligand excluded by PLIP IOD.4: 4 residues within 4Å: Chain A: F.527, L.529, C.531, P.619 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: 3 residues within 4Å: Chain A: L.753, R.808, E.812 Ligand excluded by PLIP IOD.7: 3 residues within 4Å: Chain A: S.601, A.746, D.747 Ligand excluded by PLIP IOD.8: 2 residues within 4Å: Chain A: P.506, S.811 Ligand excluded by PLIP IOD.9: 2 residues within 4Å: Chain A: R.711, E.714 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain A: P.422, L.423 Ligand excluded by PLIP

2 x ZN: ZINC ION(Non-covalent)

ZN.11: 3 residues within 4Å: Chain A: D.276, H.280, H.439 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.276, A:D.276, A:H.280, A:H.439 ZN.12: 4 residues within 4Å: Chain A: D.136, T.174, D.323, H.324 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.136, A:T.174, A:D.323, A:H.324

1 x CA: CALCIUM ION(Non-covalent)

CA.13: 6 residues within 4Å: Chain A: D.704, N.706, D.708, L.710, R.711, D.712 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.704, A:D.708, A:L.710, A:D.712

1 x 7C8: [3,5-bis(chloranyl)phenyl]methyl 4-[(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]pentyl]piperazine-1-carboxylate(Non-covalent)

7C8.14: 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 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.43, A:F.175, A:F.214, A:F.214, A:W.219, A:W.219, A:F.239, A:F.239, A:F.239 Hydrogen bonds: A:W.240 pi-Stacking: A:F.238

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

NA.15: 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:D.637

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

SCN.16: 3 residues within 4Å: Chain A: K.464, V.465, P.466 No protein-ligand interaction detected (PLIP) SCN.17: 3 residues within 4Å: Chain A: S.641, P.671, K.674 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.641 SCN.18: 6 residues within 4Å: Chain A: G.643, F.644, Y.649, W.677, A.678, Q.681 No protein-ligand interaction detected (PLIP) SCN.19: 2 residues within 4Å: Chain A: G.25, C.27 No protein-ligand interaction detected (PLIP)

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.20: 4 residues within 4Å: Chain A: A.672, R.675, D.765, N.766 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.675, A:N.766, A:N.766 GOL.21: 4 residues within 4Å: Chain A: L.341, T.342, N.343, T.371 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.342, A:N.343, A:T.371 GOL.22: 6 residues within 4Å: Chain A: N.475, A.486, P.487, N.488, G.490, H.492 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.475, A:N.488, A:N.488, A:G.490

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,Ectonucleotide pyrophosphatase/phosphodiesterase family member 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2,Ectonucleotide pyrophosphatase/phosphodiesterase family member 2

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