- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.10 Å
- Oligo State
- monomer
- Ligands
- 1 x NAG- NAG- BMA- BMA: beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
- 2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)
- 1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)
- 2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
PG4.4: 9 residues within 4Å:- Chain A: V.202, K.203, L.206, P.207, T.210
- Ligands: EDO.27, GOL.51, GOL.54, GLN.68
No protein-ligand interaction detected (PLIP)PG4.61: 4 residues within 4Å:- Chain A: S.99
- Ligands: PGE.43, CIT.60, GLN.62
2 PLIP interactions:2 Ligand-Ligand interactions- Hydrogen bonds: Q.62, Q.62
- 28 x GLN: GLUTAMINE(Non-covalent)
GLN.6: 8 residues within 4Å:- Chain A: R.8, V.39, G.43, A.44, D.45, V.83
- Ligands: GLN.7, EDO.35
10 PLIP interactions:8 interactions with chain A, 2 Ligand-Ligand interactions- Hydrophobic interactions: A:V.39
- Hydrogen bonds: A:A.44, A:A.44, A:D.45, Q.6, Q.6
- Water bridges: A:R.8, A:S.79, A:N.82
- Salt bridges: A:R.8
GLN.7: 7 residues within 4Å:- Chain A: T.4, P.5, I.6, R.8, P.125, R.126
- Ligands: GLN.6
6 PLIP interactions:4 interactions with chain A, 2 Ligand-Ligand interactions- Hydrogen bonds: A:I.6, A:I.6, A:R.8, Q.7, Q.7
- Salt bridges: A:R.126
GLN.8: 9 residues within 4Å:- Chain A: L.42, Y.275, E.277, T.286, S.294, K.297
- Ligands: GLN.19, EDO.24, GLN.76
7 PLIP interactions:6 interactions with chain A, 1 Ligand-Ligand interactions- Hydrophobic interactions: A:T.286
- Hydrogen bonds: A:T.286, A:S.294, A:K.297, Q.8
- Water bridges: A:K.297
- Salt bridges: A:K.297
GLN.9: 8 residues within 4Å:- Chain A: S.150, Q.151, Q.152, E.194, H.195, H.251
- Ligands: GLN.10, GLN.13
9 PLIP interactions:6 Ligand-Ligand interactions, 3 interactions with chain A- Hydrogen bonds: Q.9, Q.9, Q.10, A:Q.151, A:H.195
- Water bridges: Q.9, Q.9, Q.10
- Salt bridges: A:K.250
GLN.10: 6 residues within 4Å:- Chain A: K.250, H.251, R.253, K.254
- Ligands: GLN.9, EDO.30
8 PLIP interactions:6 interactions with chain A, 2 Ligand-Ligand interactions- Hydrogen bonds: A:K.250, A:K.254, A:K.254, Q.9
- Water bridges: A:H.251, Q.9
- Salt bridges: A:H.251, A:K.254
GLN.11: 9 residues within 4Å:- Chain A: L.209, T.210, K.213, V.214, T.215, N.232, G.233, L.234, P.301
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:L.209, A:T.215
- Water bridges: A:K.213, A:K.213
- Salt bridges: A:K.213
GLN.12: 9 residues within 4Å:- Chain A: V.139, T.140, G.143, N.144, P.156, R.157, N.158, L.161
- Ligands: CIT.60
8 PLIP interactions:7 interactions with chain A, 1 Ligand-Ligand interactions- Hydrophobic interactions: A:T.140
- Hydrogen bonds: A:T.140, A:G.143, A:N.144, A:R.157, A:N.158
- Water bridges: A:D.147, Q.16
GLN.13: 10 residues within 4Å:- Chain A: Q.151, E.194, H.195, D.246, K.250
- Ligands: GLN.9, PO4.20, EDO.29, PGE.42, GOL.53
6 PLIP interactions:5 interactions with chain A, 1 Ligand-Ligand interactions- Hydrogen bonds: A:Q.151, A:D.246
- Water bridges: A:E.194, A:D.246, Q.13
- Salt bridges: A:K.250
GLN.14: 6 residues within 4Å:- Chain A: R.27, F.244, M.245
- Ligands: GLN.18, PGE.42, GOL.53
6 PLIP interactions:6 interactions with chain A,- Hydrogen bonds: A:M.245
- Water bridges: A:R.27, A:R.27, A:D.246, A:D.246
- Salt bridges: A:R.27
GLN.15: 5 residues within 4Å:- Chain A: R.27, E.267, N.268, L.270
- Ligands: GOL.47
4 PLIP interactions:2 Ligand-Ligand interactions, 2 interactions with chain A- Hydrogen bonds: Q.15, Q.15, A:E.267
- Salt bridges: A:R.27
GLN.16: 6 residues within 4Å:- Chain A: D.147, F.148, R.155, P.156, R.157
- Ligands: PGE.45
9 PLIP interactions:6 interactions with chain A, 3 Ligand-Ligand interactions- Hydrophobic interactions: A:D.147, A:R.157
- Hydrogen bonds: A:D.147, A:R.155, A:R.155, Q.16, Q.16
- Salt bridges: A:R.157
- Water bridges: Q.12
GLN.17: 4 residues within 4Å:- Chain A: N.128, D.179, R.302, R.305
8 PLIP interactions:4 interactions with chain A, 4 Ligand-Ligand interactions- Hydrogen bonds: A:D.179, A:R.302, A:R.305, Q.17, Q.17, Q.17, Q.17
- Water bridges: A:N.128
GLN.18: 10 residues within 4Å:- Chain A: Y.55, F.56, H.92, H.223, F.244
- Ligands: GLN.14, PO4.20, EDO.28, EDO.29, GLN.66
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:F.244
- Hydrogen bonds: A:H.92
- Salt bridges: A:H.92
GLN.19: 9 residues within 4Å:- Chain A: E.277, I.278, T.279, E.282, M.283, S.284, K.297
- Ligands: GLN.8, EDO.24
11 PLIP interactions:2 Ligand-Ligand interactions, 9 interactions with chain A- Hydrogen bonds: Q.19, Q.19, A:E.277, A:T.279, A:S.284, A:S.284
- Hydrophobic interactions: A:T.279, A:E.282
- Water bridges: A:K.297, A:K.297
- Salt bridges: A:K.297
GLN.59: 2 residues within 4Å:- Chain A: T.164
- Ligands: GLN.62
1 PLIP interactions:1 Ligand-Ligand interactions- Hydrogen bonds: Q.62
GLN.62: 8 residues within 4Å:- Chain A: V.98, S.99, I.102, P.116, L.161
- Ligands: GLN.59, CIT.60, PG4.61
6 PLIP interactions:5 interactions with chain A, 1 Ligand-Ligand interactions- Hydrophobic interactions: A:P.116
- Hydrogen bonds: A:S.99, A:S.99, Q.59
- Water bridges: A:Y.117, A:Y.117
GLN.66: 8 residues within 4Å:- Chain A: F.56, T.57, H.92, D.146
- Ligands: GLN.18, EDO.28, GOL.52, GLN.74
7 PLIP interactions:3 Ligand-Ligand interactions, 4 interactions with chain A- Hydrogen bonds: Q.66, Q.66, Q.74
- Hydrophobic interactions: A:F.56, A:T.57
- Water bridges: A:F.56
- Salt bridges: A:H.92
GLN.67: 4 residues within 4Å:- Chain A: R.119, L.120, R.121
- Ligands: GLN.72
9 PLIP interactions:6 interactions with chain A, 3 Ligand-Ligand interactions- Hydrophobic interactions: A:L.120
- Hydrogen bonds: A:R.121, A:R.121
- Water bridges: A:N.112, A:R.119, Q.67, Q.67, Q.72
- Salt bridges: A:R.119
GLN.68: 10 residues within 4Å:- Chain A: W.190, V.202, K.203, L.206, E.231, Y.259
- Ligands: PG4.4, GOL.46, GOL.49, GOL.54
4 PLIP interactions:3 interactions with chain A, 1 Ligand-Ligand interactions- Hydrophobic interactions: A:W.190
- Hydrogen bonds: A:E.231
- Salt bridges: A:K.203
- Water bridges: Q.68
GLN.69: 4 residues within 4Å:- Chain A: K.254
- Ligands: EDO.30, GOL.46, GOL.49
9 PLIP interactions:5 interactions with chain A, 4 Ligand-Ligand interactions- Hydrophobic interactions: A:K.254
- Water bridges: A:K.254, A:K.254
- Salt bridges: A:H.199, A:K.254
- Hydrogen bonds: Q.69, Q.69, Q.69, Q.69
GLN.70: 4 residues within 4Å:- Chain A: N.268, S.269, E.289
- Ligands: EDO.32
3 PLIP interactions:3 interactions with chain A,- Hydrogen bonds: A:E.289
- Water bridges: A:L.270, A:L.270
GLN.71: 7 residues within 4Å:- Chain A: E.72, D.73, S.76, R.81, R.110
- Ligands: 1PE.5, GOL.56
6 PLIP interactions:4 Ligand-Ligand interactions, 2 interactions with chain A- Hydrogen bonds: Q.71, Q.71, Q.71, Q.71, A:D.73
- Salt bridges: A:R.110
GLN.72: 5 residues within 4Å:- Chain A: P.114, S.115, Y.118, R.119
- Ligands: GLN.67
7 PLIP interactions:6 interactions with chain A, 1 Ligand-Ligand interactions- Hydrophobic interactions: A:P.114, A:Y.118
- Hydrogen bonds: A:S.115, A:Y.117, A:R.119
- Water bridges: A:R.119, Q.67
GLN.73: 1 residues within 4Å:- Chain A: K.203
2 PLIP interactions:2 interactions with chain A,- Water bridges: A:K.203
- Salt bridges: A:K.203
GLN.74: 6 residues within 4Å:- Chain A: D.146, D.147
- Ligands: PGE.45, GOL.50, GOL.52, GLN.66
5 PLIP interactions:4 Ligand-Ligand interactions, 1 interactions with chain A- Hydrogen bonds: Q.66, Q.66, Q.74
- Water bridges: Q.66
- Salt bridges: A:R.157
GLN.75: 5 residues within 4Å:- Chain A: R.261, F.262, L.295, F.296
- Ligands: GLN.76
7 PLIP interactions:1 interactions with chain A, 6 Ligand-Ligand interactions- Hydrophobic interactions: A:F.262
- Hydrogen bonds: Q.75, Q.75, Q.75, Q.75, Q.76, Q.76
GLN.76: 8 residues within 4Å:- Chain A: S.294, L.295, F.296, K.297
- Ligands: GLN.8, EDO.24, GLN.75, GLN.77
4 PLIP interactions:3 Ligand-Ligand interactions, 1 interactions with chain A- Hydrogen bonds: Q.75, Q.75, Q.77
- Water bridges: A:K.297
GLN.77: 3 residues within 4Å:- Chain A: K.293, S.294
- Ligands: GLN.76
6 PLIP interactions:4 Ligand-Ligand interactions, 2 interactions with chain A- Hydrogen bonds: Q.76, Q.77, Q.77, A:S.294
- Water bridges: Q.77
- Hydrophobic interactions: A:K.293
- 1 x PO4: PHOSPHATE ION(Non-functional Binders)
PO4.20: 13 residues within 4Å:- Chain A: D.14, D.52, Y.55, N.91, H.92, H.195, H.221, H.223
- Ligands: GLN.13, GLN.18, EDO.29, FE.64, FE.65
11 PLIP interactions:2 Ligand-Ligand interactions, 9 interactions with chain A- Hydrogen bonds: Q.18, Q.18, A:D.14, A:N.91, A:N.91
- Water bridges: A:H.195, A:H.223
- Salt bridges: A:H.92, A:H.195, A:H.221, A:H.223
- 17 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.21: 4 residues within 4Å:- Chain A: P.207, L.208, T.211
- Ligands: P6G.3
Ligand excluded by PLIPEDO.22: 1 residues within 4Å:- Chain A: T.211
Ligand excluded by PLIPEDO.23: 1 residues within 4Å:- Ligands: P6G.3
Ligand excluded by PLIPEDO.24: 4 residues within 4Å:- Chain A: K.297
- Ligands: GLN.8, GLN.19, GLN.76
Ligand excluded by PLIPEDO.25: 6 residues within 4Å:- Chain A: T.57, G.58, V.59, H.60, G.96
- Ligands: GOL.50
Ligand excluded by PLIPEDO.26: 2 residues within 4Å:- Chain A: G.292
- Ligands: PGE.41
Ligand excluded by PLIPEDO.27: 2 residues within 4Å:- Chain A: P.207
- Ligands: PG4.4
Ligand excluded by PLIPEDO.28: 4 residues within 4Å:- Chain A: Q.151
- Ligands: GLN.18, GOL.52, GLN.66
Ligand excluded by PLIPEDO.29: 8 residues within 4Å:- Chain A: N.91, S.145, D.146, Q.151, H.195
- Ligands: GLN.13, GLN.18, PO4.20
Ligand excluded by PLIPEDO.30: 3 residues within 4Å:- Chain A: K.254
- Ligands: GLN.10, GLN.69
Ligand excluded by PLIPEDO.31: 3 residues within 4Å:- Chain A: K.106, I.107
- Ligands: GOL.56
Ligand excluded by PLIPEDO.32: 3 residues within 4Å:- Chain A: S.291, K.293
- Ligands: GLN.70
Ligand excluded by PLIPEDO.33: 4 residues within 4Å:- Chain A: A.62, A.103
- Ligands: NAG-NAG-BMA-BMA.1, NAG-NAG-BMA-BMA.1
Ligand excluded by PLIPEDO.34: 4 residues within 4Å:- Chain A: K.65, Q.68, E.69, D.73
Ligand excluded by PLIPEDO.35: 5 residues within 4Å:- Chain A: A.44, D.45, N.82, P.84
- Ligands: GLN.6
Ligand excluded by PLIPEDO.36: 2 residues within 4Å:- Ligands: NAG-NAG-BMA-BMA.1, NAG-NAG-BMA-BMA.1
Ligand excluded by PLIPEDO.37: 4 residues within 4Å:- Chain A: I.102, S.105, K.106, P.114
Ligand excluded by PLIP- 8 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
PGE.38: 5 residues within 4Å:- Chain A: A.160, R.163, T.164, A.167
- Ligands: P6G.3
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.163
PGE.39: 4 residues within 4Å:- Chain A: K.249, L.252, L.260, H.263
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:K.249, A:H.263
PGE.40: 6 residues within 4Å:- Chain A: L.141, P.156, L.166, C.200, Q.204
- Ligands: 1PE.2
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Q.204
- Water bridges: A:Q.204
PGE.41: 8 residues within 4Å:- Chain A: A.30, K.33, A.34, T.37, T.38, A.290, G.292
- Ligands: EDO.26
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:T.37
PGE.42: 6 residues within 4Å:- Chain A: E.194, D.246, S.248
- Ligands: GLN.13, GLN.14, GOL.53
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:S.248
- Water bridges: A:S.248, A:S.248
PGE.43: 6 residues within 4Å:- Chain A: H.60, G.96, N.97
- Ligands: NAG-NAG-BMA-BMA.1, CIT.60, PG4.61
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:H.60
PGE.44: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)PGE.45: 3 residues within 4Å:- Chain A: R.157
- Ligands: GLN.16, GLN.74
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.157
- 13 x GOL: GLYCEROL(Non-functional Binders)
GOL.46: 7 residues within 4Å:- Chain A: R.253, K.254, V.255, P.256
- Ligands: GOL.49, GLN.68, GLN.69
No protein-ligand interaction detected (PLIP)GOL.47: 4 residues within 4Å:- Chain A: T.25, A.26, R.27
- Ligands: GLN.15
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:A.26, A:R.27
- Water bridges: A:R.27, A:R.27
GOL.48: 5 residues within 4Å:- Chain A: A.36, T.37, K.40, D.77, P.78
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:A.36, A:S.79
- Water bridges: A:K.40
GOL.49: 7 residues within 4Å:- Chain A: W.190, H.199, V.202, K.254
- Ligands: GOL.46, GLN.68, GLN.69
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:H.199, A:K.254
- Water bridges: A:K.203, A:K.203
GOL.50: 3 residues within 4Å:- Chain A: L.95
- Ligands: EDO.25, GLN.74
No protein-ligand interaction detected (PLIP)GOL.51: 4 residues within 4Å:- Chain A: T.210, N.232
- Ligands: PG4.4, GOL.54
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:N.232
- Water bridges: A:T.210
GOL.52: 7 residues within 4Å:- Chain A: D.146, F.148, V.149, Q.151
- Ligands: EDO.28, GLN.66, GLN.74
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:Q.151
GOL.53: 3 residues within 4Å:- Ligands: GLN.13, GLN.14, PGE.42
No protein-ligand interaction detected (PLIP)GOL.54: 10 residues within 4Å:- Chain A: W.190, L.206, T.210, D.230, E.231, N.232, Y.259
- Ligands: PG4.4, GOL.51, GLN.68
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:D.230, A:E.231, A:N.232
GOL.55: 7 residues within 4Å:- Chain A: L.252, V.255, P.256, N.257, G.258, Y.259, L.260
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:V.255, A:G.258, A:Y.259, A:L.260
GOL.56: 7 residues within 4Å:- Chain A: Q.68, E.72, Y.104, I.107
- Ligands: 1PE.5, EDO.31, GLN.71
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Q.68, A:E.72
GOL.57: 6 residues within 4Å:- Chain A: R.81, N.82, V.83, P.84, K.109, R.110
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:N.82
- Water bridges: A:K.109
GOL.58: 5 residues within 4Å:- Chain A: D.147, F.148, V.149, S.150, E.154
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:V.149, A:S.150, A:E.154
- 1 x CIT: CITRIC ACID(Non-functional Binders)
- 1 x NA: SODIUM ION(Non-functional Binders)
- 2 x FE: FE (III) ION(Non-covalent)
FE.64: 6 residues within 4Å:- Chain A: D.14, D.52, Y.55, H.223
- Ligands: PO4.20, FE.65
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
FE.65: 7 residues within 4Å:- Chain A: D.14, D.52, N.91, H.186, H.221
- Ligands: PO4.20, FE.64
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
- 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
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.10 Å
- Oligo State
- monomer
- Ligands
- 1 x NAG- NAG- BMA- BMA: beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
- 2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)
- 1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)
- 2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
- 28 x GLN: GLUTAMINE(Non-covalent)
- 1 x PO4: PHOSPHATE ION(Non-functional Binders)
- 17 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 8 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)
- 13 x GOL: GLYCEROL(Non-functional Binders)
- 1 x CIT: CITRIC ACID(Non-functional Binders)
- 1 x NA: SODIUM ION(Non-functional Binders)
- 2 x FE: FE (III) ION(Non-covalent)
- 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