SMTL ID : 7z0n.1

Structure-Based Design of a Novel Class of Autotaxin Inhibitors Based on Endogenous Allosteric Modulators

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 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: 24 residues within 4Å: Chain A: L.165, Y.166, E.168, S.169, H.170, G.171, G.200, G.201, Q.202, K.210, H.378, N.381, N.382, R.383, R.384, A.466, P.467, N.468, N.469, D.688, G.689, L.690, H.776 Ligands: MAN.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.202

1 x MAN: alpha-D-mannopyranose(Non-functional Binders)

MAN.2: 1 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.1 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 6 residues within 4Å: Chain A: D.256, H.260, H.304, M.306, H.419 Ligands: I8K.21 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.256, A:D.256, A:H.260, A:H.419, H2O.1 ZN.4: 7 residues within 4Å: Chain A: D.116, G.117, T.154, D.303, H.304, H.419 Ligands: I8K.21 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.116, A:D.116, A:T.154, A:D.303, A:H.304

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain A: D.684, N.686, D.688, L.690, D.692 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.684, A:D.688, A:L.690, A:D.692, H2O.4

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

IOD.6: 7 residues within 4Å: Chain A: K.153, G.174, N.175, S.176, V.330, L.334, R.336 Ligand excluded by PLIP IOD.7: 7 residues within 4Å: Chain A: S.176, M.177, Y.178, S.185, H.187, V.330, R.338 Ligand excluded by PLIP IOD.8: 2 residues within 4Å: Chain A: P.99, P.108 Ligand excluded by PLIP IOD.9: 6 residues within 4Å: Chain A: P.732, L.733, R.788, E.792, I.793, L.796 Ligand excluded by PLIP

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

SCN.10: 4 residues within 4Å: Chain A: T.594, Y.622, G.623, K.654 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.654 SCN.11: 5 residues within 4Å: Chain A: K.25, S.26, S.221, V.222, S.223 No protein-ligand interaction detected (PLIP) SCN.12: 3 residues within 4Å: Chain A: K.440, Y.441, R.480 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.440 SCN.13: 5 residues within 4Å: Chain A: P.144, K.444, V.445, P.446, P.447 No protein-ligand interaction detected (PLIP) SCN.14: 4 residues within 4Å: Chain A: K.25, S.28, S.29, C.30 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.30 SCN.20: 4 residues within 4Å: Chain A: V.392, D.393, R.394, V.425 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.392 SCN.22: 6 residues within 4Å: Chain A: G.14, P.15, P.16, D.17, R.19, S.29 No protein-ligand interaction detected (PLIP) SCN.24: 5 residues within 4Å: Chain A: L.23, T.217, F.218, F.219 Ligands: I8K.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.219

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

NA.15: 4 residues within 4Å: Chain A: Y.614, D.617, M.620, S.621 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.614 NA.16: 4 residues within 4Å: Chain A: N.746, D.747, S.749, S.752 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.747, A:S.749, A:S.752

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.17: 4 residues within 4Å: Chain A: P.486, T.487, M.488, Y.790 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.488 GOL.18: 14 residues within 4Å: Chain A: C.68, L.69, G.72, D.73, C.74, C.75, T.76, L.231, L.234, Q.235, S.238, G.286, Q.289, L.290 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.68, A:C.74, A:C.74, A:Q.289 GOL.19: 5 residues within 4Å: Chain A: K.582, S.670, E.671, N.673, F.722 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.582, A:N.673 GOL.23: 9 residues within 4Å: Chain A: L.158, Y.159, A.162, W.199, W.205, F.218, F.219, Y.251 Ligands: I8K.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.158

1 x I8K: [4-[1-[(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]piperidin-4-yl]oxyphenyl]-bis(oxidanyl)-$l^{4}-borane(Covalent)

I8K.21: 32 residues within 4Å: Chain A: L.23, Y.27, D.116, K.153, T.154, F.155, Y.159, N.175, L.188, R.189, K.193, F.194, N.195, H.196, W.199, P.203, W.205, I.206, F.219, W.220, V.222, Y.251, E.253, D.256, H.260, D.303, H.304, H.419 Ligands: ZN.3, ZN.4, GOL.23, SCN.24 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.155, A:F.155, A:L.188, A:F.194, A:F.194, A:W.199, A:W.199, A:F.219, A:F.219 Hydrogen bonds: A:Y.27, A:Y.27, A:D.116, A:T.154, A:N.175, A:W.205, A:H.419

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clark, J.M. et al., Structure-Based Design of a Novel Class of Autotaxin Inhibitors Based on Endogenous Allosteric Modulators. J.Med.Chem. (2022)

Release Date

2022-05-04

Peptides

Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2