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SMTL ID : 5s9l.1

AUTOTAXIN, 4-[3-Oxo-3-(2-oxo-2,3-dihydro-benzooxazol-6-yl)-propyl]-piperazine-1-carboxylic acid 3,5-dichloro-benzyl ester, 1.90A, P212121, Rfree=19.1%

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-MAN-MAN-MAN-MAN-MAN.1:

13 residues within 4Å:

Chain A: L.193, E.196, S.197, H.198, G.228, N.409, N.410, P.495, N.496, N.497, D.716, L.718, H.804

No protein-ligand interaction detected (PLIP)

2 x CA: CALCIUM ION(Non-covalent)

CA.2:	4 residues within 4Å: Chain A: D.144, T.182, D.331, H.332 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.144, A:T.182, A:D.331, A:H.332
CA.10:	5 residues within 4Å: Chain A: D.712, N.714, D.716, L.718, D.720 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.712, A:D.716, A:L.718, A:D.720, H₂O.17

1 x K: POTASSIUM ION(Non-covalent)

K.3:	4 residues within 4Å: Chain A: Y.642, D.645, M.648 Ligands: ACT.5 6 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: A:Y.642, A:D.645, A:M.648, ACT.5, H₂O.10, H₂O.17

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

ACT.4:	4 residues within 4Å: Chain A: V.420, D.421, R.422, V.453 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.422 Salt bridges: A:R.422
ACT.5:	4 residues within 4Å: Chain A: Y.642, M.648, S.649 Ligands: K.3 No protein-ligand interaction detected (PLIP)
ACT.6:	7 residues within 4Å: Chain A: K.181, G.202, N.203, S.204, V.358, L.362, R.364 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.358, A:L.362 Hydrogen bonds: A:N.203, A:S.204 Salt bridges: A:K.181, A:R.364

1 x 6ZO: (3,5-dichlorophenyl)methyl 4-[3-oxo-3-(2-oxo-2,3-dihydro-1,3-benzoxazol-6-yl)propyl]piperazine-1-carboxylate(Non-covalent)

6ZO.7:

17 residues within 4Å:

Chain A: I.140, S.142, D.144, T.182, F.183, L.186, N.203, L.216, W.233, F.246, F.247, W.248, Y.279, D.284, H.288, H.447
Ligands: ZN.8

5 PLIP interactions:

5 interactions with chain A

Hydrophobic interactions: A:T.182, A:L.216
Hydrogen bonds: A:N.203, A:W.248
pi-Stacking: A:F.247

1 x ZN: ZINC ION(Non-covalent)

ZN.8:

4 residues within 4Å:

Chain A: D.284, H.288, H.447
Ligands: 6ZO.7

4 PLIP interactions:

4 interactions with chain A

Metal complexes: A:D.284, A:D.284, A:H.288, A:H.447

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

NA.9:

4 residues within 4Å:

Chain A: N.774, D.775, S.777, S.780

3 PLIP interactions:

3 interactions with chain A

Hydrogen bonds: A:S.780, A:S.780
Water bridges: A:S.780

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Hunziker, D. et al., Synthesis, Characterization, and in vivo Evaluation of a Novel Potent Autotaxin-Inhibitor. Front Pharmacol (2021)

Release Date

2022-04-13

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Isoform 2 of Ectonucleotide pyrophosphatase/phosphodiesterase family member 2

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