SMTL ID : 7p0k.1

Crystal structure of Autotaxin (ENPP2) with 18F-labeled positron emission tomography ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x 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

NAG-BMA-MAN-MAN-MAN-MAN-MAN.1: 16 residues within 4Å: Chain A: L.165, E.168, S.169, H.170, G.171, G.200, G.201, Q.202, K.210, N.377, N.378, R.379, A.452, P.453, L.656 Ligands: NAG.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.165

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 13 residues within 4Å: Chain A: L.165, Y.166, E.168, S.169, H.374, P.453, N.454, N.455, D.654, G.655, L.656, H.742 Ligands: NAG-BMA-MAN-MAN-MAN-MAN-MAN.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.453, A:N.455 Water bridges: A:S.169

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

SCN.3: 6 residues within 4Å: Chain A: Y.483, P.484, I.522, L.523, Y.524, R.568 No protein-ligand interaction detected (PLIP) SCN.4: 4 residues within 4Å: Chain A: W.205, T.217, F.218 Ligands: 4I0.11 1 PLIP interactions: 1 interactions with chain A Water bridges: A:W.205 SCN.14: 3 residues within 4Å: Chain A: T.310, D.312, R.313 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.310, A:R.313

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: D.256, H.260, H.304, M.306, H.405 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.405, H2O.1 ZN.6: 6 residues within 4Å: Chain A: D.116, G.117, T.154, D.303, H.304, H.405 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.116, A:T.154, A:D.303, A:H.304, H2O.1

1 x CA: CALCIUM ION(Non-covalent)

CA.7: 5 residues within 4Å: Chain A: D.650, N.652, D.654, L.656, D.658 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.650, A:D.654, A:L.656, A:D.658, H2O.6

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

IOD.8: 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.9: 6 residues within 4Å: Chain A: S.176, M.177, Y.178, H.187, V.330, R.338 Ligand excluded by PLIP IOD.10: 4 residues within 4Å: Chain A: F.492, L.494, C.496, P.565 Ligand excluded by PLIP IOD.12: 7 residues within 4Å: Chain A: R.505, T.545, S.547, G.640, P.691, A.692, D.693 Ligand excluded by PLIP IOD.13: 5 residues within 4Å: Chain A: R.471, P.472, S.755, Y.756, S.757 Ligand excluded by PLIP

1 x 4I0: 2-[[2-ethyl-6-[4-[2-[(3~{R})-3-fluoranylpyrrolidin-1-yl]-2-oxidanylidene-ethyl]piperazin-1-yl]imidazo[1,2-a]pyridin-3-yl]-methyl-amino]-4-(4-fluorophenyl)-2,3-dihydro-1,3-thiazole-5-carbonitrile(Non-covalent)

4I0.11: 26 residues within 4Å: Chain A: L.23, Y.27, I.112, S.114, T.154, F.155, L.158, Y.159, L.161, A.162, K.193, F.194, H.196, W.199, G.201, P.203, W.205, I.206, F.218, F.219, W.220, A.249, F.250, Y.251, M.443 Ligands: SCN.4 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.112, A:T.154, A:F.155, A:A.162, A:F.194, A:F.219, A:F.219, A:Y.251 Hydrogen bonds: A:W.205 pi-Stacking: A:F.218 Halogen bonds: A:G.201

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deng, X. et al., Imaging Autotaxin In Vivo with 18 F-Labeled Positron Emission Tomography Ligands. J Med Chem (2021)

Release Date

2022-07-13

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