SMTL ID : 7ov3.1

Crystal structure of pig purple acid phosphatase in complex with Maybridge fragment CC063346, dimethyl sulfoxide and citrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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.1: 6 residues within 4Å: Chain A: H.60, D.61, A.62, N.97, A.100 Ligands: EDO.30 No protein-ligand interaction detected (PLIP)

8 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.2: 5 residues within 4Å: Chain A: P.156, L.159, A.162, R.163, Q.204 No protein-ligand interaction detected (PLIP) DMS.3: 5 residues within 4Å: Chain A: F.56, H.223, F.244 Ligands: PGE.6, CIT.18 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.244 DMS.4: 4 residues within 4Å: Chain A: D.146, D.147, V.149 Ligands: R2J.10 1 PLIP interactions: 1 interactions with chain A Water bridges: A:F.148 DMS.5: 4 residues within 4Å: Chain A: R.253, K.254, V.255, P.256 No protein-ligand interaction detected (PLIP) DMS.8: 5 residues within 4Å: Chain A: V.39, K.40, T.41, L.42, G.43 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.44 DMS.12: 3 residues within 4Å: Chain A: L.120, R.121, F.122 No protein-ligand interaction detected (PLIP) DMS.13: 4 residues within 4Å: Chain A: L.42, E.277, T.286, K.297 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.286 Salt bridges: A:E.277 DMS.26: 4 residues within 4Å: Chain A: K.254 Ligands: PGE.7, R2J.9, EDO.29 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.254

5 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.6: 7 residues within 4Å: Chain A: R.27, F.244, M.245, D.246 Ligands: DMS.3, CIT.18, CIT.19 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.27, A:M.245 Water bridges: A:R.27, A:R.27, A:R.27, A:D.246 PGE.7: 5 residues within 4Å: Chain A: K.250 Ligands: R2J.9, PGE.25, DMS.26, EDO.29 No protein-ligand interaction detected (PLIP) PGE.14: 3 residues within 4Å: Chain A: V.149, S.150 Ligands: R2J.10 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.149 PGE.24: 5 residues within 4Å: Chain A: S.115, Y.117, Y.118, T.164, W.168 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.115 PGE.25: 2 residues within 4Å: Ligands: PGE.7, R2J.9 No protein-ligand interaction detected (PLIP)

3 x R2J: N-methyl-1-(1-methyl-1H-indazol-3-yl)methanamine(Non-covalent)

R2J.9: 8 residues within 4Å: Chain A: Q.152, K.250, H.251, K.254 Ligands: PGE.7, PGE.25, DMS.26, EDO.29 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.254 R2J.10: 5 residues within 4Å: Chain A: D.147, F.148, V.149 Ligands: DMS.4, PGE.14 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.148, A:V.149 R2J.11: 5 residues within 4Å: Chain A: K.249, H.263, F.264, G.265, A.266 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.249, A:G.265 Water bridges: A:K.249, A:H.263

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

NAG.15: 1 residues within 4Å: Chain A: N.128 No protein-ligand interaction detected (PLIP)

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.16: 9 residues within 4Å: Chain A: D.52, Y.55, N.91, H.92, H.195, H.221, H.223 Ligands: FE.27, FE.28 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:D.14, A:N.91 Water bridges: A:H.92, A:H.92, A:H.186, A:H.195, A:H.221, A:H.223 Salt bridges: A:H.92, A:H.195, A:H.221, A:H.223

5 x CIT: CITRIC ACID(Non-functional Binders)

CIT.17: 7 residues within 4Å: Chain A: H.94, G.96, N.97, V.98, S.99, R.157 Ligands: NA.32 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.98, A:S.99 Water bridges: A:R.157, A:R.157 Salt bridges: A:H.94, A:R.157 CIT.18: 3 residues within 4Å: Chain A: Q.151 Ligands: DMS.3, PGE.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.151, A:Q.151 CIT.19: 2 residues within 4Å: Chain A: E.267 Ligands: PGE.6 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.267, A:E.267 CIT.20: 11 residues within 4Å: Chain A: A.176, E.178, D.179, Y.180, V.181, H.212, K.213, V.214, T.215, R.303, A.304 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:K.213 Hydrogen bonds: A:E.178, A:V.181, A:H.212, A:R.303 Water bridges: A:R.303, A:R.303, A:R.303 Salt bridges: A:R.303 CIT.21: 2 residues within 4Å: Chain A: R.119, R.121 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.119 Water bridges: A:R.121, A:R.121, A:R.121 Salt bridges: A:R.119, A:R.121, A:K.171

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.22: 5 residues within 4Å: Chain A: L.206, T.210, E.231, N.232, Y.259 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.210, A:N.232 Water bridges: A:D.230, A:Y.259, A:Y.259 GOL.23: 2 residues within 4Å: Chain A: Q.68, I.107 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.68 Water bridges: A:Q.68, A:I.107, A:S.108, A:K.109

2 x FE: FE (III) ION(Non-covalent)

FE.27: 7 residues within 4Å: Chain A: D.14, D.52, N.91, H.186, H.221 Ligands: PO4.16, FE.28 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.52, A:H.186, A:H.221, H2O.1 FE.28: 6 residues within 4Å: Chain A: D.14, D.52, Y.55, H.223 Ligands: PO4.16, FE.27 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.14, A:D.52, A:Y.55, A:H.223, H2O.1

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.29: 5 residues within 4Å: Chain A: R.253, K.254 Ligands: PGE.7, R2J.9, DMS.26 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.254 EDO.30: 5 residues within 4Å: Chain A: A.62, K.63, A.103 Ligands: NAG-NAG.1, NAG-NAG.1 No protein-ligand interaction detected (PLIP) EDO.31: 2 residues within 4Å: Chain A: K.106, I.107 No protein-ligand interaction detected (PLIP)

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

NA.32: 3 residues within 4Å: Chain A: H.94, G.96 Ligands: CIT.17 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.94

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.33: 4 residues within 4Å: Chain A: Q.152, P.197, T.198, H.199 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feder, D. et al., Rational Design of Potent Inhibitors of a Metallohydrolase Using a Fragment-Based Approach. Chemmedchem (2021)

Release Date

2022-01-12

Peptides

Tartrate-resistant acid phosphatase type 5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Tartrate-resistant acid phosphatase type 5

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