Receptor
PDB id Resolution Class Description Source Keywords
3N9R 1.8 Å EC: 4.1.2.13 CLASS II FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE FROM HELICOBACTE IN COMPLEX WITH N-(4-HYDROXYBUTYL)-PHOSPHOGLYCOLOHYDROXAMICC OMPETITIVE INHIBITOR HELICOBACTER PYLORI FBP ALDOLASE CLASS II INHIBITOR LYASE
Ref.: RATIONAL DESIGN, SYNTHESIS, AND EVALUATION OF NEW S INHIBITORS OF MICROBIAL CLASS II (ZINC DEPENDENT) F BIS-PHOSPHATE ALDOLASES. J.MED.CHEM. V. 53 7836 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:310;
B:310;
K:310;
P:310;
U:310;
Z:310;
E:310;
J:310;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
 submit data
35.453 Cl [Cl-]
NA A:309;
B:309;
K:309;
P:309;
U:309;
Z:309;
E:309;
J:309;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
none;
none;
none;
none;
 submit data
22.99 Na [Na+]
TD3 A:311;
B:311;
K:311;
P:311;
U:311;
Z:311;
E:311;
J:311;
 Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
none;
none;
none;
none;
 Ki = 5.5 uM
243.152 C6 H14 N O7 P C(CCO...
ZN A:308;
B:308;
K:308;
P:308;
U:308;
Z:308;
E:308;
J:308;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
none;
none;
none;
none;
 submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3C56 2.3 Å EC: 4.1.2.13 CLASS II FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE FROM HELICOBACTE IN COMPLEX WITH N-(3-HYDROXYPROPYL)-GLYCOLOHYDROXAMIC ACID B ISPHOSPHATE, A COMPETITIVE INHIBITOR HELICOBACTER PYLORI CLASS II FBP ALDOLASE GLYCOLYSIS INHIBITOR LYASE METALZINC
Ref.: SYNTHESIS AND BIOCHEMICAL EVALUATION OF SELECTIVE I OF CLASS II FRUCTOSE BISPHOSPHATE ALDOLASES: TOWARD SYNTHETIC ANTIBIOTICS. CHEMISTRY V. 14 8521 2008
Members (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 13 families.
1 5UD0 - G3H C3 H7 O6 P C([C@H](C=....
2 3C52 - PGH C2 H6 N O6 P C(C(=O)NO)....
3 5UCK - 13P C3 H7 O6 P C(C(=O)COP....
4 5UCN - 13P C3 H7 O6 P C(C(=O)COP....
5 3N9R Ki = 5.5 uM TD3 C6 H14 N O7 P C(CCO)CN(C....
6 5VJF - 13P C3 H7 O6 P C(C(=O)COP....
7 3N9S Ki = 0.07 uM TD4 C6 H15 N O10 P2 C(CCOP(=O)....
8 5UD2 - 13P C3 H7 O6 P C(C(=O)COP....
9 5UD4 - P6T C6 H14 O12 P2 C([C@H]([C....
10 5UCP - G3H C3 H7 O6 P C([C@H](C=....
11 5UD3 - P6F C6 H14 O12 P2 C([C@H]([C....
12 3C56 Ki = 0.013 uM PH4 C5 H13 N O10 P2 C(CN(C(=O)....
13 5UCZ - 13P C3 H7 O6 P C(C(=O)COP....
70% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 5UD0 - G3H C3 H7 O6 P C([C@H](C=....
2 3C52 - PGH C2 H6 N O6 P C(C(=O)NO)....
3 5UCK - 13P C3 H7 O6 P C(C(=O)COP....
4 5UCN - 13P C3 H7 O6 P C(C(=O)COP....
5 3N9R Ki = 5.5 uM TD3 C6 H14 N O7 P C(CCO)CN(C....
6 5VJF - 13P C3 H7 O6 P C(C(=O)COP....
7 3N9S Ki = 0.07 uM TD4 C6 H15 N O10 P2 C(CCOP(=O)....
8 5UD2 - 13P C3 H7 O6 P C(C(=O)COP....
9 5UD4 - P6T C6 H14 O12 P2 C([C@H]([C....
10 5UCP - G3H C3 H7 O6 P C([C@H](C=....
11 5UD3 - P6F C6 H14 O12 P2 C([C@H]([C....
12 3C56 Ki = 0.013 uM PH4 C5 H13 N O10 P2 C(CN(C(=O)....
13 5UCZ - 13P C3 H7 O6 P C(C(=O)COP....
50% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4TO8 ic50 = 56.9 mM FLC C6 H5 O7 C(C(=O)[O-....
2 5UD0 - G3H C3 H7 O6 P C([C@H](C=....
3 3C52 - PGH C2 H6 N O6 P C(C(=O)NO)....
4 5UCK - 13P C3 H7 O6 P C(C(=O)COP....
5 5UCN - 13P C3 H7 O6 P C(C(=O)COP....
6 3N9R Ki = 5.5 uM TD3 C6 H14 N O7 P C(CCO)CN(C....
7 5VJF - 13P C3 H7 O6 P C(C(=O)COP....
8 3N9S Ki = 0.07 uM TD4 C6 H15 N O10 P2 C(CCOP(=O)....
9 5UD2 - 13P C3 H7 O6 P C(C(=O)COP....
10 5UD4 - P6T C6 H14 O12 P2 C([C@H]([C....
11 5UCP - G3H C3 H7 O6 P C([C@H](C=....
12 5UD3 - P6F C6 H14 O12 P2 C([C@H]([C....
13 3C56 Ki = 0.013 uM PH4 C5 H13 N O10 P2 C(CN(C(=O)....
14 5UCZ - 13P C3 H7 O6 P C(C(=O)COP....
15 2ISW Ki = 37 nM PGH C2 H6 N O6 P C(C(=O)NO)....
16 3GAY Kd = 20 nM P6T C6 H14 O12 P2 C([C@H]([C....
17 3OHI Ki = 14 uM HDX C8 H13 N O9 P2 C1=CN(C(=O....
18 3GB6 - P6F C6 H14 O12 P2 C([C@H]([C....
19 2ISV Ki = 37 nM PGH C2 H6 N O6 P C(C(=O)NO)....
20 1GVF - PGH C2 H6 N O6 P C(C(=O)NO)....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: TD3; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 TD3 1 1
2 TD4 0.681818 0.98
3 PH4 0.636364 0.960784
Similar Ligands (3D)
Ligand no: 1; Ligand: TD3; Similar ligands found: 1
No: Ligand Similarity coefficient
1 PAZ 0.8607
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3C56; Ligand: PH4; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3c56.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3C56; Ligand: PH4; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3c56.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
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