SMTL ID : 5inh.1

Crystal structure of Autotaxin/ENPP2 with a covalent fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-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.1: 17 residues within 4Å: Chain A: L.229, S.233, H.234, F.246, H.260, R.261, W.262, W.263, G.264, G.265, R.448, P.531, N.532, N.533, N.752, L.754, H.840 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.754 Water bridges: A:G.265

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 3 residues within 4Å: Chain A: N.62, S.64, P.80 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: D.180, T.218, D.367, H.368 Ligands: 6C1.8 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.180, A:D.180, A:T.218, A:D.367, A:H.368 ZN.4: 5 residues within 4Å: Chain A: D.320, H.324, H.483 Ligands: ACT.7, 6C1.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.320, A:D.320, A:H.324, A:H.483

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain A: D.748, N.750, N.752, L.754, D.756 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.748, A:L.754, A:D.756, H2O.9

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

NAG.6: 4 residues within 4Å: Chain A: L.385, T.386, I.416, N.419 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.416 Hydrogen bonds: A:T.386, A:T.386, A:N.419

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 6 residues within 4Å: Chain A: N.239, D.320, H.324, H.483 Ligands: ZN.4, 6C1.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.239 Salt bridges: A:K.217, A:H.324, A:H.483

1 x 6C1: {2-[(3-chlorophenyl)methoxy]phenyl}boronic acid(Covalent)

6C1.8: 16 residues within 4Å: Chain A: D.180, K.217, T.218, F.219, N.239, L.252, Y.315, E.317, D.320, F.321, H.324, H.368, H.483 Ligands: ZN.3, ZN.4, ACT.7 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.218, A:F.219, A:L.252, A:E.317, A:F.321 Hydrogen bonds: A:T.218, A:N.239, A:Y.315

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lanier, M. et al., Repurposing Suzuki Coupling Reagents as a Directed Fragment Library Targeting Serine Hydrolases and Related Enzymes. J. Med. Chem. (2017)

Release Date

2017-03-15

Peptides

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2