- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.00 Å
- Oligo State
- homo-dimer
- Ligands
- 3 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose
- 1 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose
- 2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 1 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose
- 1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 1 x NAG- FUC: alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 2 x ZN: ZINC ION(Non-covalent)
ZN.10: 7 residues within 4Å:- Chain A: D.131, D.160, N.197, H.282, H.319
- Ligands: FE.11, R9X.40
4 PLIP interactions:3 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.160, A:H.282, A:H.319, H2O.1
ZN.41: 7 residues within 4Å:- Chain B: D.131, D.160, N.197, H.282, H.319
- Ligands: FE.42, R9X.75
4 PLIP interactions:3 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.160, B:H.282, B:H.319, H2O.26
- 2 x FE: FE (III) ION(Non-covalent)
FE.11: 7 residues within 4Å:- Chain A: D.131, D.160, Y.163, H.319, H.321
- Ligands: ZN.10, R9X.40
5 PLIP interactions:4 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.131, A:D.160, A:Y.163, A:H.321, H2O.1
FE.42: 7 residues within 4Å:- Chain B: D.131, D.160, Y.163, H.319, H.321
- Ligands: ZN.41, R9X.75
5 PLIP interactions:4 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:D.131, B:D.160, B:Y.163, B:H.321, H2O.26
- 5 x FLC: CITRATE ANION(Non-covalent)
FLC.12: 4 residues within 4Å:- Chain A: V.269, K.270, R.271, S.272
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:R.271, A:S.272
- Water bridges: A:R.271
- Salt bridges: A:H.420
FLC.14: 4 residues within 4Å:- Chain A: R.108, R.109, F.110, Y.188
8 PLIP interactions:8 interactions with chain A- Hydrophobic interactions: A:F.110
- Hydrogen bonds: A:Y.188, A:Y.188, A:Y.188
- Water bridges: A:R.109, A:E.183
- Salt bridges: A:R.108, A:R.108
FLC.15: 3 residues within 4Å:- Chain A: W.56, K.63, R.109
9 PLIP interactions:9 interactions with chain A- Hydrophobic interactions: A:W.56
- Hydrogen bonds: A:W.56, A:K.63, A:R.109
- Water bridges: A:K.63, A:R.109
- Salt bridges: A:K.63, A:R.109, A:R.109
FLC.16: 6 residues within 4Å:- Chain A: N.290, H.291, I.364, D.365, S.366, N.367
10 PLIP interactions:10 interactions with chain A- Hydrophobic interactions: A:H.291, A:N.367
- Hydrogen bonds: A:N.290, A:S.366, A:N.367, A:N.367
- Water bridges: A:H.292, A:S.366, A:N.367
- Salt bridges: A:H.291
FLC.43: 6 residues within 4Å:- Chain B: N.290, H.291, D.365, S.366, N.367
- Ligands: GOL.74
9 PLIP interactions:9 interactions with chain B- Hydrophobic interactions: B:N.290, B:H.291, B:N.367
- Hydrogen bonds: B:N.290, B:S.366, B:N.367
- Water bridges: B:H.291, B:D.365
- Salt bridges: B:H.291
- 3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
PGE.13: 10 residues within 4Å:- Chain A: T.301, N.331, I.332, A.333, Y.334
- Chain B: M.294, E.297
- Ligands: SO4.19, EDO.27, PGE.44
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:I.332, A:Y.334
- Water bridges: A:R.300, A:R.300
PGE.17: 4 residues within 4Å:- Chain A: R.166
- Ligands: SO4.26, GOL.35, R9X.40
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.166
PGE.44: 12 residues within 4Å:- Chain A: R.300, N.331, Y.334, C.341
- Chain B: R.300, T.301, N.331, Y.334, L.340, C.341
- Ligands: PGE.13, GOL.58
8 PLIP interactions:5 interactions with chain B, 3 interactions with chain A- Hydrogen bonds: B:R.300, B:R.300, B:N.331, B:C.341, A:R.300, A:N.331, A:C.341
- Water bridges: B:Y.334
- 18 x SO4: SULFATE ION(Non-functional Binders)
SO4.18: 3 residues within 4Å:- Chain A: R.36, K.92, Y.93
Ligand excluded by PLIPSO4.19: 5 residues within 4Å:- Chain A: R.254, Y.259, K.302
- Chain B: E.295
- Ligands: PGE.13
Ligand excluded by PLIPSO4.20: 4 residues within 4Å:- Chain A: W.415
- Ligands: NAG-NAG-BMA-MAN-FUC.4, NAG-NAG-BMA-MAN-FUC.4, NAG-NAG-BMA-MAN-FUC.4
Ligand excluded by PLIPSO4.21: 4 residues within 4Å:- Chain A: M.368, Q.370, Q.372, R.379
Ligand excluded by PLIPSO4.22: 4 residues within 4Å:- Chain A: V.34, R.36, Y.93, Q.117
Ligand excluded by PLIPSO4.23: 2 residues within 4Å:- Chain A: V.344, K.345
Ligand excluded by PLIPSO4.24: 2 residues within 4Å:- Chain A: K.3, R.5
Ligand excluded by PLIPSO4.25: 2 residues within 4Å:- Chain A: R.64, I.65
Ligand excluded by PLIPSO4.26: 4 residues within 4Å:- Chain A: R.166, Y.361
- Ligands: PGE.17, R9X.40
Ligand excluded by PLIPSO4.47: 3 residues within 4Å:- Chain B: K.270, R.271, S.272
Ligand excluded by PLIPSO4.48: 3 residues within 4Å:- Chain B: R.267, K.309, Y.310
Ligand excluded by PLIPSO4.49: 1 residues within 4Å:- Chain B: R.402
Ligand excluded by PLIPSO4.50: 4 residues within 4Å:- Chain B: N.4, R.166, Y.167, P.168
Ligand excluded by PLIPSO4.51: 2 residues within 4Å:- Chain B: V.344, K.345
Ligand excluded by PLIPSO4.52: 3 residues within 4Å:- Chain B: R.36, K.92, Y.93
Ligand excluded by PLIPSO4.53: 3 residues within 4Å:- Chain B: R.36, Y.93, Q.117
Ligand excluded by PLIPSO4.54: 3 residues within 4Å:- Chain B: N.2, K.3, R.5
Ligand excluded by PLIPSO4.55: 2 residues within 4Å:- Chain B: K.3, R.5
Ligand excluded by PLIP- 2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.27: 4 residues within 4Å:- Chain A: K.335
- Ligands: PGE.13, GOL.30, GOL.73
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:K.335
- Water bridges: A:K.335
EDO.57: 2 residues within 4Å:- Chain B: L.9, D.10
4 PLIP interactions:4 interactions with chain B- Water bridges: B:L.9, B:L.9, B:L.9, B:D.10
- 25 x GOL: GLYCEROL(Non-functional Binders)
GOL.28: 5 residues within 4Å:- Chain A: M.45, S.79, S.80, G.81, F.82
Ligand excluded by PLIPGOL.29: 3 residues within 4Å:- Chain A: E.210, K.213
- Ligands: NAG-FUC.9
Ligand excluded by PLIPGOL.30: 6 residues within 4Å:- Chain A: K.335
- Chain B: N.290, F.293, I.369
- Ligands: EDO.27, GOL.73
Ligand excluded by PLIPGOL.31: 3 residues within 4Å:- Chain A: K.345, D.346, Q.347
Ligand excluded by PLIPGOL.32: 4 residues within 4Å:- Chain A: E.58, N.94, K.96, I.113
Ligand excluded by PLIPGOL.33: 3 residues within 4Å:- Chain A: L.33, Q.227, K.268
Ligand excluded by PLIPGOL.34: 2 residues within 4Å:- Chain A: R.402, Q.404
Ligand excluded by PLIPGOL.35: 5 residues within 4Å:- Chain A: N.4, R.166, Y.167, P.168
- Ligands: PGE.17
Ligand excluded by PLIPGOL.36: 5 residues within 4Å:- Chain A: R.254, G.255, Y.259, K.263
- Ligands: R9X.75
Ligand excluded by PLIPGOL.37: 4 residues within 4Å:- Chain A: H.397, E.410, S.413, W.415
Ligand excluded by PLIPGOL.58: 9 residues within 4Å:- Chain A: M.294, E.297
- Chain B: R.300, T.301, N.331, I.332, A.333, Y.334
- Ligands: PGE.44
Ligand excluded by PLIPGOL.59: 2 residues within 4Å:- Chain B: D.346, S.348
Ligand excluded by PLIPGOL.60: 5 residues within 4Å:- Chain B: K.391, W.415
- Ligands: NAG-NAG-BMA-FUC.7, NAG-NAG-BMA-FUC.7, GOL.65
Ligand excluded by PLIPGOL.61: 4 residues within 4Å:- Chain B: M.368, Q.370, Q.372, R.379
Ligand excluded by PLIPGOL.62: 4 residues within 4Å:- Chain B: L.9, Y.167, D.171, R.174
Ligand excluded by PLIPGOL.63: 3 residues within 4Å:- Chain B: K.263, K.264, R.267
Ligand excluded by PLIPGOL.64: 3 residues within 4Å:- Chain A: P.204, E.205
- Chain B: K.264
Ligand excluded by PLIPGOL.65: 5 residues within 4Å:- Chain B: K.391, H.397, E.410, W.415
- Ligands: GOL.60
Ligand excluded by PLIPGOL.66: 2 residues within 4Å:- Chain B: S.50, R.104
Ligand excluded by PLIPGOL.67: 4 residues within 4Å:- Chain A: E.295
- Chain B: R.254, Y.259, K.302
Ligand excluded by PLIPGOL.68: 3 residues within 4Å:- Chain B: W.56, K.63, R.109
Ligand excluded by PLIPGOL.69: 2 residues within 4Å:- Chain B: P.231, F.232
Ligand excluded by PLIPGOL.72: 5 residues within 4Å:- Chain B: T.1, N.2, R.166, Y.361
- Ligands: R9X.75
Ligand excluded by PLIPGOL.73: 5 residues within 4Å:- Chain B: N.290, F.293
- Ligands: EDO.27, GOL.30, GOL.74
Ligand excluded by PLIPGOL.74: 2 residues within 4Å:- Ligands: FLC.43, GOL.73
Ligand excluded by PLIP- 3 x CL: CHLORIDE ION(Non-functional Binders)
- 1 x NA: SODIUM ION(Non-functional Binders)
- 2 x R9X: [(R)-(decanoylamino)-naphthalen-1-yl-methyl]phosphonic acid(Non-covalent)
R9X.40: 16 residues within 4Å:- Chain A: D.160, Y.163, D.165, R.166, N.197, H.198, H.291, H.292, H.319, H.321, Y.361
- Chain B: R.254
- Ligands: ZN.10, FE.11, PGE.17, SO4.26
8 PLIP interactions:7 interactions with chain A, 1 interactions with chain B- Hydrophobic interactions: A:D.165, A:Y.361
- Hydrogen bonds: A:N.197, A:H.291, A:H.321
- Water bridges: A:Y.361, A:Y.361
- pi-Cation interactions: B:R.254
R9X.75: 16 residues within 4Å:- Chain A: R.254
- Chain B: D.160, Y.163, D.165, R.166, N.197, H.198, H.291, H.292, H.319, H.321, Y.361
- Ligands: GOL.36, ZN.41, FE.42, GOL.72
10 PLIP interactions:10 interactions with chain B- Hydrophobic interactions: B:R.166, B:Y.361
- Hydrogen bonds: B:N.197, B:H.291, B:H.292, B:H.321, B:H.321, B:Y.361
- Water bridges: B:D.160
- pi-Stacking: B:H.292
- 1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- 2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
NAG.46: 6 residues within 4Å:- Chain B: S.57, N.60, R.62, R.64, K.92, Y.97
6 PLIP interactions:6 interactions with chain B- Hydrophobic interactions: B:R.62
- Hydrogen bonds: B:S.57, B:R.64, B:R.64, B:Y.97
- Water bridges: B:T.95
NAG.56: 3 residues within 4Å:- Chain B: P.204, E.205, N.207
1 PLIP interactions:1 interactions with chain B- Water bridges: B:N.207
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Feder, D. et al., Optimization of an alpha-aminonaphthylmethylphosphonic acid inhibitor of purple acid phosphatase using rational structure-based design approaches. Eur.J.Med.Chem. (2023)
- Release Date
- 2023-08-02
- Peptides
- Fe(3+)-Zn(2+) purple acid phosphatase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
BB
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.00 Å
- Oligo State
- homo-dimer
- Ligands
- 3 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose
- 1 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose
- 2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 1 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose
- 1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 1 x NAG- FUC: alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- 2 x ZN: ZINC ION(Non-covalent)
- 2 x FE: FE (III) ION(Non-covalent)
- 5 x FLC: CITRATE ANION(Non-covalent)
- 3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
- 18 x SO4: SULFATE ION(Non-functional Binders)
- 2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 25 x GOL: GLYCEROL(Non-functional Binders)
- 3 x CL: CHLORIDE ION(Non-functional Binders)
- 1 x NA: SODIUM ION(Non-functional Binders)
- 2 x R9X: [(R)-(decanoylamino)-naphthalen-1-yl-methyl]phosphonic acid(Non-covalent)
- 1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- 2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Feder, D. et al., Optimization of an alpha-aminonaphthylmethylphosphonic acid inhibitor of purple acid phosphatase using rational structure-based design approaches. Eur.J.Med.Chem. (2023)
- Release Date
- 2023-08-02
- Peptides
- Fe(3+)-Zn(2+) purple acid phosphatase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
BB
D