SMTL ID : 8brn.1 (1 other biounit)

Crystal structure of red kidney bean purple acid phosphatase in complex with an alpha-aminonaphthylmethylphosphonic acid inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

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: 7 residues within 4Å: Chain A: M.7, S.11, D.12, V.13, F.136, N.139, S.143 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.12

1 x NAG- NAG- BMA- MAN- MAN- FUC: alpha-D-mannopyranose-(1-2)-[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

NAG-NAG-BMA-MAN-MAN-FUC.2: 4 residues within 4Å: Chain A: F.76, N.77, P.168, N.169 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.168

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

NAG-NAG-BMA-FUC.3: 3 residues within 4Å: Chain A: Y.20, R.104, N.105 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-FUC.7: 3 residues within 4Å: Chain B: Y.20, R.104, N.105 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.104 NAG-NAG-BMA-FUC.8: 7 residues within 4Å: Chain B: K.391, N.392, R.393, T.394, H.395, W.415 Ligands: GOL.65 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.395

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

NAG-NAG-BMA-MAN-MAN-FUC.4: 7 residues within 4Å: Chain A: K.391, N.392, T.394, H.395, W.415 Ligands: GOL.27, FLC.38 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.415

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.5: 7 residues within 4Å: Chain B: M.7, S.11, D.12, V.13, F.136, N.139, S.143 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.15

1 x NAG- NAG- BMA- FUC: beta-D-mannopyranose-(5-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUC.6: 4 residues within 4Å: Chain B: F.76, N.77, P.168, N.169 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.168

2 x ZN: ZINC ION(Non-covalent)

ZN.9: 7 residues within 4Å: Chain A: D.131, D.160, N.197, H.282, H.319 Ligands: FE.10, 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.2 ZN.46: 7 residues within 4Å: Chain B: D.131, D.160, N.197, H.282, H.319 Ligands: FE.47, R9X.73 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.160, B:H.282, B:H.319, H2O.28

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

FE.10: 7 residues within 4Å: Chain A: D.131, D.160, Y.163, H.319, H.321 Ligands: ZN.9, 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.2 FE.47: 7 residues within 4Å: Chain B: D.131, D.160, Y.163, H.319, H.321 Ligands: ZN.46, R9X.73 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.28

8 x FLC: CITRATE ANION(Non-covalent)(Non-functional Binders)

FLC.11: 6 residues within 4Å: Chain A: N.290, H.291, I.364, D.365, S.366, N.367 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:H.291 Hydrogen bonds: A:D.365, A:S.366, A:N.367, A:N.367 Water bridges: A:N.290, A:H.291, A:I.364, A:I.364, A:D.365 Salt bridges: A:H.291 FLC.13: 2 residues within 4Å: Chain A: L.120, R.393 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.393 Salt bridges: A:R.393, A:R.393, A:R.393 FLC.38: 3 residues within 4Å: Ligands: NAG-NAG-BMA-MAN-MAN-FUC.4, NAG-NAG-BMA-MAN-MAN-FUC.4, GOL.27 No protein-ligand interaction detected (PLIP) FLC.41: 4 residues within 4Å: Chain B: K.309, Y.310, K.311 Ligands: GOL.64 8 PLIP interactions: 8 interactions with chain B Water bridges: B:Y.310, B:Y.310, B:Y.310, B:K.311, B:H.420 Salt bridges: B:K.309, B:K.311, B:H.420 FLC.42: 6 residues within 4Å: Chain B: N.290, H.291, I.364, D.365, S.366, N.367 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:H.291 Hydrogen bonds: B:D.365, B:D.365, B:S.366, B:N.367, B:N.367 Water bridges: B:N.290 Salt bridges: B:H.291 FLC.43: 5 residues within 4Å: Chain B: N.4, D.6, R.166, Y.167, P.168 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.167, B:Y.167 Hydrogen bonds: B:R.166 Water bridges: B:N.2, B:N.4, B:N.4, B:R.5, B:R.5, B:R.166, B:R.166 Salt bridges: B:R.166, B:R.166 FLC.67: 2 residues within 4Å: Chain B: K.309 Ligands: GOL.64 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.309 Salt bridges: B:K.309, B:K.309 FLC.68: 2 residues within 4Å: Chain B: R.402, Q.404 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Q.404 Hydrogen bonds: B:Q.404 Water bridges: B:S.382, B:S.382, B:R.402 Salt bridges: B:R.402, B:R.402, B:R.402

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

PGE.12: 3 residues within 4Å: Chain A: R.5, F.136 Ligands: SO4.21 1 PLIP interactions: 1 interactions with chain A Water bridges: A:F.136 PGE.15: 8 residues within 4Å: Chain A: R.254, G.255, Y.259, T.260, K.263, R.267 Ligands: R9X.72, R9X.73 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.255, A:K.263, A:R.267 Water bridges: A:R.254, A:K.263, B:N.197, B:N.197 PGE.44: 4 residues within 4Å: Chain B: G.152, Q.153, Y.188, Q.189 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.189 Water bridges: B:K.96

3 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)(Post Translational Modification)

NAG.14: 1 residues within 4Å: Chain A: N.207 No protein-ligand interaction detected (PLIP) NAG.45: 4 residues within 4Å: Chain B: P.204, E.205, N.207 Ligands: NAG.56 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.204 NAG.56: 2 residues within 4Å: Chain B: N.207 Ligands: NAG.45 No protein-ligand interaction detected (PLIP)

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

SO4.16: 5 residues within 4Å: Chain A: M.368, Q.370, Q.372, R.379 Ligands: GOL.29 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.370, A:Q.372 Water bridges: A:Q.372, A:Q.372, A:Q.372 Salt bridges: A:R.379 SO4.17: 4 residues within 4Å: Chain A: K.270, R.271, S.272, H.420 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.270, A:R.271, A:S.272 Water bridges: A:S.272, A:S.272 Salt bridges: A:K.270, A:H.420 SO4.18: 5 residues within 4Å: Chain A: S.57, N.60, R.64, K.92, Y.97 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.57, A:N.60 Water bridges: A:S.57 Salt bridges: A:R.64, A:K.92 SO4.19: 1 residues within 4Å: Chain A: R.402 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Q.404, A:Q.404, A:Q.404 Salt bridges: A:R.402 SO4.20: 3 residues within 4Å: Chain A: R.36, K.92, Y.93 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.93, A:Y.93 Salt bridges: A:R.36 SO4.21: 2 residues within 4Å: Chain A: R.5 Ligands: PGE.12 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.5 Salt bridges: A:R.5 SO4.48: 5 residues within 4Å: Chain A: E.295 Chain B: R.254, Y.259, K.302 Ligands: GOL.70 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.259 Water bridges: B:Y.259 Salt bridges: B:R.254, B:K.302 SO4.49: 3 residues within 4Å: Chain B: N.2, K.3, R.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.2, B:K.3 Water bridges: B:R.5 Salt bridges: B:R.5 SO4.50: 4 residues within 4Å: Chain B: P.343, V.344, K.345, E.374 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.345, B:E.374 Water bridges: B:P.343 Salt bridges: B:K.345 SO4.51: 2 residues within 4Å: Chain B: K.3, R.5 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.3, B:R.5 SO4.52: 3 residues within 4Å: Chain B: K.270, R.271, S.272 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.271, B:S.272 Water bridges: B:H.420 SO4.53: 4 residues within 4Å: Chain B: K.59, N.60, R.62, R.64 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.60, B:R.62 Water bridges: B:S.57, B:R.64 Salt bridges: B:K.59, B:R.64 SO4.54: 2 residues within 4Å: Chain B: K.92, Y.93 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.93 Salt bridges: B:K.92 SO4.55: 4 residues within 4Å: Chain B: K.150, K.391, W.415 Ligands: GOL.65 7 PLIP interactions: 7 interactions with chain B Water bridges: B:K.150, B:K.150, B:H.397, B:H.397 Salt bridges: B:K.150, B:K.391, B:H.397

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

EDO.22: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.57: 1 residues within 4Å: Chain B: N.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.4 Water bridges: B:N.4, B:N.4

25 x GOL: GLYCEROL(Non-functional Binders)

GOL.23: 8 residues within 4Å: Chain A: R.300, T.301, N.331, I.332, A.333, Y.334 Chain B: M.294, E.297 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain A: K.311, Q.347, S.348, R.419, P.423 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain A: K.391, H.397, E.410, W.415 Ligands: GOL.27, GOL.32 Ligand excluded by PLIP GOL.26: 3 residues within 4Å: Chain A: P.149, K.150, D.389 Ligand excluded by PLIP GOL.27: 7 residues within 4Å: Chain A: K.391, W.415 Ligands: NAG-NAG-BMA-MAN-MAN-FUC.4, NAG-NAG-BMA-MAN-MAN-FUC.4, GOL.25, GOL.32, FLC.38 Ligand excluded by PLIP GOL.28: 5 residues within 4Å: Chain A: N.4, D.6, R.166, Y.167, P.168 Ligand excluded by PLIP GOL.29: 5 residues within 4Å: Chain A: Q.372, A.377, F.378, R.379 Ligands: SO4.16 Ligand excluded by PLIP GOL.30: 3 residues within 4Å: Chain A: K.309, Y.310 Ligands: GOL.34 Ligand excluded by PLIP GOL.31: 3 residues within 4Å: Chain A: K.3, R.5 Ligands: GOL.39 Ligand excluded by PLIP GOL.32: 6 residues within 4Å: Chain A: H.397, S.413, V.414, W.415 Ligands: GOL.25, GOL.27 Ligand excluded by PLIP GOL.33: 3 residues within 4Å: Chain A: S.50, A.52, L.103 Ligand excluded by PLIP GOL.34: 3 residues within 4Å: Chain A: K.309 Ligands: GOL.30, GOL.35 Ligand excluded by PLIP GOL.35: 6 residues within 4Å: Chain A: K.263, R.267, K.309, Y.310 Ligands: GOL.34, R9X.73 Ligand excluded by PLIP GOL.39: 5 residues within 4Å: Chain A: K.3, Y.361, V.363 Ligands: GOL.31, R9X.40 Ligand excluded by PLIP GOL.58: 4 residues within 4Å: Chain B: M.368, Q.370, Q.372, R.379 Ligand excluded by PLIP GOL.59: 5 residues within 4Å: Chain A: R.300, Y.334 Chain B: R.300, N.331, Y.334 Ligand excluded by PLIP GOL.60: 3 residues within 4Å: Chain B: K.335, T.337, N.338 Ligand excluded by PLIP GOL.61: 4 residues within 4Å: Chain B: S.366, N.367, M.368, Q.370 Ligand excluded by PLIP GOL.62: 4 residues within 4Å: Chain B: S.71, S.216, Y.217, H.220 Ligand excluded by PLIP GOL.63: 2 residues within 4Å: Chain B: G.406, V.407 Ligand excluded by PLIP GOL.64: 5 residues within 4Å: Chain B: R.267, K.309, Y.310 Ligands: FLC.41, FLC.67 Ligand excluded by PLIP GOL.65: 5 residues within 4Å: Chain B: K.391, W.415 Ligands: NAG-NAG-BMA-FUC.8, NAG-NAG-BMA-FUC.8, SO4.55 Ligand excluded by PLIP GOL.69: 2 residues within 4Å: Chain B: R.254 Ligands: GOL.70 Ligand excluded by PLIP GOL.70: 5 residues within 4Å: Chain B: R.254, Y.259, W.306 Ligands: SO4.48, GOL.69 Ligand excluded by PLIP GOL.71: 2 residues within 4Å: Ligands: R9X.72, R9X.73 Ligand excluded by PLIP

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

CL.36: 6 residues within 4Å: Chain A: G.49, S.50, G.102, L.103, R.104, N.105 Ligand excluded by PLIP CL.37: 5 residues within 4Å: Chain A: G.253, R.254, K.302 Chain B: Y.249, E.295 Ligand excluded by PLIP CL.66: 5 residues within 4Å: Chain A: Y.249, E.295 Chain B: G.253, R.254, K.302 Ligand excluded by PLIP

3 x R9X: [(R)-(decanoylamino)-naphthalen-1-yl-methyl]phosphonic acid(Non-covalent)

R9X.40: 14 residues within 4Å: Chain A: K.3, Y.163, R.166, N.197, H.198, H.291, H.292, H.319, H.321, Y.361 Chain B: R.254 Ligands: ZN.9, FE.10, GOL.39 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.197, A:H.198, A:H.291, A:H.292, A:H.319 Water bridges: A:Y.163, A:Y.361 pi-Stacking: A:H.292, A:H.292 R9X.72: 11 residues within 4Å: Chain A: R.254 Chain B: Y.163, N.197, H.198, H.291, H.292, H.321, Y.361 Ligands: PGE.15, GOL.71, R9X.73 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.321 Water bridges: B:H.321 R9X.73: 15 residues within 4Å: Chain A: R.254, K.263 Chain B: D.160, N.197, H.198, H.291, H.292, H.319, H.321 Ligands: PGE.15, GOL.35, ZN.46, FE.47, GOL.71, R9X.72 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.197, B:H.198, B:H.291 Water bridges: B:H.319, B:H.319

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
A

B
C

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

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