SMTL ID : 6g46.1

Red kidney bean purple acid phosphatase in complex with 2-(Naphthalen-1-yl)thiazole-4-carboxylic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

6 x NAG- FUC- NAG: alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-FUC-NAG.1: 5 residues within 4Å: Chain A: N.75, P.166, N.167 Chain D: Y.18, D.44 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:P.166 Water bridges: D:D.44 NAG-FUC-NAG.2: 3 residues within 4Å: Chain A: Y.18, R.102, N.103 No protein-ligand interaction detected (PLIP) NAG-FUC-NAG.3: 5 residues within 4Å: Chain A: K.389, N.390, T.392, H.393, W.413 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.413 NAG-FUC-NAG.5: 4 residues within 4Å: Chain B: K.389, N.390, H.393, W.413 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.413 NAG-FUC-NAG.6: 7 residues within 4Å: Chain C: K.389, N.390, R.391, T.392, H.393, W.413, Y.420 1 PLIP interactions: 1 interactions with chain C Water bridges: C:H.393 Hydrophobic interactions: C:W.413 NAG-FUC-NAG.9: 6 residues within 4Å: Chain D: K.389, N.390, R.391, T.392, H.393, W.413 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.413

3 x NAG- FUC: alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.4: 3 residues within 4Å: Chain B: Y.18, R.102, N.103 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.18 NAG-FUC.7: 3 residues within 4Å: Chain C: Y.18, R.102, N.103 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.18 Hydrogen bonds: C:R.102, C:N.103 NAG-FUC.8: 3 residues within 4Å: Chain D: Y.18, R.102, N.103 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:Y.18 Hydrogen bonds: D:N.103 Water bridges: D:R.102

4 x ZN: ZINC ION(Non-covalent)

ZN.10: 7 residues within 4Å: Chain A: D.129, D.158, N.195, H.280, H.317 Ligands: FE.11, ELH.15 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.158, A:H.280, A:H.317 ZN.17: 7 residues within 4Å: Chain B: D.129, D.158, N.195, H.280, H.317 Ligands: FE.18, ELH.23 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.158, B:H.280, B:H.317 ZN.30: 7 residues within 4Å: Chain C: D.129, D.158, N.195, H.280, H.317 Ligands: FE.31, SO4.36 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.158, C:H.280, C:H.317 ZN.39: 7 residues within 4Å: Chain D: D.129, D.158, N.195, H.280, H.317 Ligands: FE.40, SO4.43 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.158, D:H.280, D:H.317

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

FE.11: 6 residues within 4Å: Chain A: D.129, D.158, Y.161, H.319 Ligands: ZN.10, ELH.15 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.129, A:D.158, A:Y.161, A:H.319 FE.18: 6 residues within 4Å: Chain B: D.129, D.158, Y.161, H.319 Ligands: ZN.17, ELH.23 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.129, B:D.158, B:Y.161, B:H.319 FE.31: 7 residues within 4Å: Chain C: D.129, D.158, Y.161, H.317, H.319 Ligands: ZN.30, SO4.36 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.129, C:D.158, C:Y.161, C:H.319 FE.40: 6 residues within 4Å: Chain D: D.129, D.158, Y.161, H.319 Ligands: ZN.39, SO4.43 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.129, D:D.158, D:Y.161, D:H.319

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.12: 4 residues within 4Å: Chain A: S.55, N.58, R.62, Y.95 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.55, A:N.58, A:Y.95 Water bridges: A:S.55, A:S.55 Salt bridges: A:R.62 SO4.13: 4 residues within 4Å: Chain A: K.268, R.269, S.270, H.418 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.269, A:S.270, A:S.270 Water bridges: A:V.267 Salt bridges: A:K.268 SO4.19: 4 residues within 4Å: Chain B: V.267, K.268, R.269, S.270 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.269, B:S.270 SO4.22: 3 residues within 4Å: Chain B: R.34, K.90, Y.91 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.91 Salt bridges: B:R.34 SO4.32: 3 residues within 4Å: Chain C: K.268, R.269, S.270 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.269, C:S.270 SO4.36: 13 residues within 4Å: Chain C: D.129, D.158, Y.161, N.195, H.196, H.280, H.289, H.290, H.317, H.319 Ligands: ZN.30, FE.31, EDO.38 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Y.161, C:N.195 Salt bridges: C:H.196, C:H.290, C:H.317, C:H.319 SO4.43: 11 residues within 4Å: Chain D: D.129, D.158, Y.161, N.195, H.196, H.289, H.290, H.317, H.319 Ligands: ZN.39, FE.40 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.195, D:N.195 Salt bridges: D:H.196, D:H.290, D:H.317, D:H.319 SO4.44: 8 residues within 4Å: Chain B: Y.247, Y.250, S.281, E.293 Chain D: G.251, R.252, K.300 Ligands: NA.24 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:Y.247, B:Y.247, B:Y.250, B:S.281, B:E.293, D:R.252 Water bridges: B:A.296 Salt bridges: D:K.300

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

NAG.14: 7 residues within 4Å: Chain A: M.5, S.9, D.10, V.11, F.134, N.137, S.141 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.134 Hydrogen bonds: A:D.10, A:D.10, A:N.137, A:S.141 NAG.20: 5 residues within 4Å: Chain B: N.75, N.167 Chain C: Y.18, D.44, E.45 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.167 NAG.21: 6 residues within 4Å: Chain B: M.5, D.10, V.11, F.134, N.137, S.141 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.134 Hydrogen bonds: B:D.10, B:D.10, B:S.141 Water bridges: B:D.10, B:D.10 NAG.33: 7 residues within 4Å: Chain C: M.5, S.9, D.10, V.11, F.134, N.137, S.141 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.10, C:D.10, C:N.137, C:S.141 NAG.35: 5 residues within 4Å: Chain B: Y.18, D.44, E.45 Chain C: N.75, N.167 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.167, B:Y.18 NAG.41: 4 residues within 4Å: Chain A: Y.18, D.44 Chain D: N.75, N.167 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:N.167, A:Y.18 NAG.42: 7 residues within 4Å: Chain D: M.5, S.9, D.10, V.11, F.134, N.137, S.141 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.134 Hydrogen bonds: D:D.10, D:D.10, D:N.137, D:S.141 Water bridges: D:D.10

2 x ELH: 2-naphthalen-1-yl-1,3-thiazole-4-carboxylic acid(Non-covalent)

ELH.15: 13 residues within 4Å: Chain A: D.129, D.158, Y.161, N.195, H.196, H.289, H.290, H.317, H.319, Y.359 Chain C: R.252 Ligands: ZN.10, FE.11 6 PLIP interactions: 6 interactions with chain A Salt bridges: A:H.196, A:H.280, A:H.290, A:H.317, A:H.319 pi-Stacking: A:H.289 ELH.23: 13 residues within 4Å: Chain B: D.129, D.158, Y.161, N.195, H.196, H.289, H.290, H.317, H.319, Y.359 Chain D: R.252 Ligands: ZN.17, FE.18 5 PLIP interactions: 5 interactions with chain B Salt bridges: B:H.196, B:H.290, B:H.317, B:H.319 pi-Stacking: B:H.289

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

EDO.16: 4 residues within 4Å: Chain A: K.148, K.389, H.395, W.413 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.148, A:K.389, A:K.389, A:H.395 EDO.27: 2 residues within 4Å: Chain B: K.65, R.102 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.65, B:K.65, B:R.102 EDO.28: 3 residues within 4Å: Chain B: R.391, T.392, W.419 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.391 EDO.29: 3 residues within 4Å: Chain B: K.343, D.344, Q.345 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.345 EDO.34: 4 residues within 4Å: Chain C: S.69, S.214, Y.215, H.218 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.69, C:S.214, C:H.218 EDO.38: 5 residues within 4Å: Chain A: R.252 Chain C: N.195, H.289, H.290 Ligands: SO4.36 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:N.195, C:N.195, C:H.289, A:R.252 EDO.45: 2 residues within 4Å: Chain D: K.61, R.107 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.61, D:K.61, D:R.107, D:R.107

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

NA.24: 5 residues within 4Å: Chain B: Y.247, S.281, E.293, H.317 Ligands: SO4.44 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.247, B:Y.247, B:S.281, B:E.293 Water bridges: B:G.294 NA.25: 5 residues within 4Å: Chain B: G.251, R.252, K.300 Chain D: Y.247, E.293 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:R.252, B:K.300, B:K.300 Water bridges: D:S.281 NA.37: 4 residues within 4Å: Chain A: E.293 Chain C: G.251, R.252, K.300 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Water bridges: A:E.293 Hydrogen bonds: C:R.252, C:K.300, C:K.300

1 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.26: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.46: 1 residues within 4Å: Chain D: K.307 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.307

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hussein, W.M. et al., Purple acid phosphatase inhibitors as leads for osteoporosis chemotherapeutics. Eur J Med Chem (2018)

Release Date

2018-09-26

Peptides

Fe(3+)-Zn(2+) purple acid phosphatase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
C

Fe(3+)-Zn(2+) purple acid phosphatase

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