Receptor
PDB id Resolution Class Description Source Keywords
3C56 2.3 Å EC: 4.1.2.13 CLASS II FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE FROM HELICOBACTER PYLORI IN COMPLEX WITH N-(3-HYDROXYPROPYL)- G LYCOLOHYDROXAMIC ACID BISPHOSPHATE, A COMPETITIVE IN HIBITOR HELICOBACTER PYLORI CLASS II FBP ALDOLASE GLYCOLYSIS INHIBITOR LYASE METAL-BINDING ZINC
Ref.: SYNTHESIS AND BIOCHEMICAL EVALUATION OF SELECTIVE INHIBITORS OF CLASS II FRUCTOSE BISPHOSPHATE ALDOLASES: TOWARDS NEW SYNTHETIC ANTIBIOTICS. CHEMISTRY V. 14 8521 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PH4 A:309;
B:309;
Valid;
Valid;
none;
none;
Ki = 0.013 uM
309.105 C5 H13 N O10 P2 C(CN(...
ZN A:308;
B:308;
Part of Protein;
Part of Protein;
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 HELICOBACTER PYLORI IN COMPLEX WITH N-(3-HYDROXYPROPYL)- G LYCOLOHYDROXAMIC ACID BISPHOSPHATE, A COMPETITIVE IN HIBITOR HELICOBACTER PYLORI CLASS II FBP ALDOLASE GLYCOLYSIS INHIBITOR LYASE METAL-BINDING ZINC
Ref.: SYNTHESIS AND BIOCHEMICAL EVALUATION OF SELECTIVE INHIBITORS OF CLASS II FRUCTOSE BISPHOSPHATE ALDOLASES: TOWARDS NEW SYNTHETIC ANTIBIOTICS. CHEMISTRY V. 14 8521 2008
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 12 families.
1 3C52 - PGH C2 H6 N O6 P C(C(=O)NO)....
2 3N9S Ki = 0.07 uM TD4 C6 H15 N O10 P2 C(CCOP(=O)....
3 3C56 Ki = 0.013 uM PH4 C5 H13 N O10 P2 C(CN(C(=O)....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 3C52 - PGH C2 H6 N O6 P C(C(=O)NO)....
2 3N9S Ki = 0.07 uM TD4 C6 H15 N O10 P2 C(CCOP(=O)....
3 3C56 Ki = 0.013 uM PH4 C5 H13 N O10 P2 C(CN(C(=O)....
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 4TO8 ic50 = 56.9 mM FLC C6 H5 O7 C(C(=O)[O-....
2 2ISW Ki = 37 nM PGH C2 H6 N O6 P C(C(=O)NO)....
3 3GAY Kd = 20 nM P6T C6 H14 O12 P2 C([C@H]([C....
4 3OHI Ki = 14 uM HDX C8 H13 N O9 P2 C1=CN(C(=O....
5 3GB6 - P6F C6 H14 O12 P2 C([C@H]([C....
6 2ISV Ki = 37 nM PGH C2 H6 N O6 P C(C(=O)NO)....
7 3C52 - PGH C2 H6 N O6 P C(C(=O)NO)....
8 3N9S Ki = 0.07 uM TD4 C6 H15 N O10 P2 C(CCOP(=O)....
9 3C56 Ki = 0.013 uM PH4 C5 H13 N O10 P2 C(CN(C(=O)....
10 1GVF - PGH C2 H6 N O6 P C(C(=O)NO)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PH4; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 PH4 1 1
2 TD4 0.761905 0.98
3 TD3 0.636364 0.960784
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3C56; Ligand: PH4; Similar sites found: 52
This union binding pocket(no: 1) in the query (biounit: 3c56.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1I7A FLC 0.01242 0.40511 None
2 2G77 AF3 0.0271 0.40064 1.62866
3 4IP7 FLC 0.02403 0.40314 1.9544
4 4JLS 3ZE 0.007578 0.43229 1.97368
5 3C8F MT2 0.00801 0.4225 2.04082
6 4Q4K FMN 0.001612 0.4347 2.28013
7 2Z48 A2G 0.01204 0.4172 2.28013
8 3GDN HBX 0.02387 0.40788 2.28013
9 3GDN FAD 0.01761 0.40788 2.28013
10 5A5W GUO 0.001521 0.45307 2.37154
11 1UJP CIT 0.003024 0.42159 2.58303
12 1LYX PGA 0.001033 0.41768 2.82258
13 1OVD FMN 0.01239 0.40829 2.9316
14 4I9B 1KA 0.01143 0.40453 2.9316
15 4WZ6 ATP 0.004535 0.44277 3.10345
16 2D2F ADP 0.006818 0.43718 3.2
17 2OMN IPH 0.02147 0.40669 3.22581
18 1YKJ FAD 0.02009 0.41743 3.25733
19 1YKJ PHB 0.02009 0.41743 3.25733
20 4K91 SIN 0.01096 0.4164 3.58306
21 5CSS G3P 0.0009759 0.40126 3.58306
22 3B5J 12D 0.002493 0.45359 3.7037
23 4YMZ 13P 0.001899 0.454 3.98406
24 4RLQ 3SK 0.0235 0.40365 4.56026
25 5EYW PGA 0.004155 0.43708 4.81928
26 2OG2 MLI 0.03164 0.41879 4.88599
27 1QDS PGA 0.0033 0.43709 5.17928
28 2WHX ADP 0.005074 0.44015 5.21173
29 3OVR 5SP 0.002119 0.41059 5.70175
30 2G30 ALA ALA PHE 0.0157 0.40226 5.81395
31 3QIN P1Y 0.03211 0.40676 6
32 2YPI PGA 0.005766 0.42532 6.07287
33 3EYK EYK 0.03883 0.41713 6.18893
34 1YQT ADP 0.01669 0.41195 6.18893
35 5F7U GLC GLC 0.01631 0.41082 6.18893
36 1JI0 ATP 0.003835 0.44403 6.25
37 3NHB ADP 0.00376 0.44717 7.49186
38 4EWN 0VR 0.002178 0.43201 7.50988
39 4NAE 1GP 0.003559 0.44528 7.55556
40 4ORM 2V6 0.01504 0.42354 7.81759
41 4ORM FMN 0.01504 0.42354 7.81759
42 4ORM ORO 0.01504 0.42354 7.81759
43 2YMZ LAT 0.01606 0.40082 8.46154
44 4KCT PYR 0.01356 0.41145 8.46906
45 3TW1 AHN 0.01686 0.41207 8.86076
46 3QH2 3NM 0.02163 0.4055 9.04977
47 1M5W DXP 0.02313 0.404 9.46502
48 2FLI DX5 0.002906 0.41679 10
49 4CZ1 VNJ 0.003694 0.44246 10.5263
50 2BTM PGA 0.004423 0.43573 20.6349
51 1KBJ FMN 0.008911 0.40237 25.0814
52 1SW0 PGA 0.008843 0.41213 25.4032
Pocket No.: 2; Query (leader) PDB : 3C56; Ligand: PH4; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
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