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
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
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 12 families.
1 3N9R Ki = 5.5 uM TD3 C6 H14 N O7 P C(CCO)CN(C....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 3N9R Ki = 5.5 uM TD3 C6 H14 N O7 P C(CCO)CN(C....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 3N9R Ki = 5.5 uM TD3 C6 H14 N O7 P C(CCO)CN(C....
Polypharmacology
Similar Ligands
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 Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3N9R; Ligand: TD3; Similar sites found: 72
This union binding pocket(no: 1) in the query (biounit: 3n9r.bio3) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2Z6I FMN 0.001199 0.46228 1.9544
2 2FK8 SAM 0.01037 0.41466 1.9544
3 4Q4K FMN 0.0003536 0.49385 2.28013
4 4XP7 FNR 0.006455 0.42107 2.28013
5 5A5W GUO 0.002739 0.46639 2.37154
6 4J36 FAD 0.02177 0.41342 2.60586
7 3NTY 5P3 0.03506 0.40946 2.60586
8 3NTY NAP 0.03373 0.40946 2.60586
9 4RGQ 13P 0.04259 0.40228 2.60586
10 1JJ7 ADP 0.009168 0.41334 2.69231
11 1OVD FMN 0.008403 0.43798 2.9316
12 1OVD ORO 0.008403 0.43798 2.9316
13 4HA6 FAD 0.04764 0.40488 2.9316
14 3OIX FMN 0.0207 0.40305 2.9316
15 1CZR FMN 0.006233 0.4218 2.95858
16 4WZ6 ATP 0.001372 0.45609 3.10345
17 1KPG SAH 0.007413 0.42349 3.13589
18 1Z2I NAD 0.02073 0.40857 3.25733
19 2CWH NDP 0.02405 0.40656 3.25733
20 1PZ1 NAP 0.02796 0.40199 3.25733
21 5CSS G3P 0.0002693 0.4675 3.58306
22 4IGH 1EA 0.02833 0.42949 3.58306
23 4IGH FMN 0.02833 0.42949 3.58306
24 4IGH ORO 0.02833 0.42949 3.58306
25 3MJY IJZ 0.01035 0.42882 3.58306
26 3MJY FMN 0.01035 0.42882 3.58306
27 3NTA COA 0.02961 0.40652 3.58306
28 3B5J 12D 0.001702 0.44816 3.7037
29 3H7R NAP 0.01226 0.42138 3.90879
30 2V58 LZJ 0.03928 0.40855 3.90879
31 2PZE ATP 0.0006462 0.47415 3.93013
32 4YMZ 13P 0.001074 0.45205 3.98406
33 4IXH IMP 0.01139 0.41592 4.23453
34 1D4D FAD 0.04434 0.40655 4.23453
35 3BW2 FMN 0.02979 0.42828 4.56026
36 5EYW PGA 0.001824 0.44102 4.81928
37 3LXD FAD 0.0205 0.41689 4.88599
38 4NZ6 DLY 0.01183 0.41634 4.88599
39 1O94 AMP 0.01757 0.4 5.21173
40 3BXF 13P 0.005429 0.42271 5.4902
41 3BXF FBP 0.01081 0.41204 5.4902
42 3OVR 5SP 0.002228 0.4491 5.70175
43 5EOU ATP 0.01741 0.40363 5.86319
44 2YPI PGA 0.002384 0.43031 6.07287
45 1YQT ADP 0.008827 0.4131 6.18893
46 5EB4 FAD 0.04921 0.40164 6.18893
47 1JI0 ATP 0.006765 0.41863 6.25
48 1TRD PGH 0.03541 0.40249 6.4
49 1OX5 1PR 0.01996 0.4094 6.51466
50 5FBK TCR 0.01131 0.4076 6.51466
51 3QVP FAD 0.04975 0.40387 6.51466
52 1AG9 FMN 0.002833 0.43833 6.85714
53 1OBV FMN 0.004469 0.4307 7.10059
54 3NHB ADP 0.001809 0.41446 7.49186
55 4EWN 0VR 0.001116 0.42292 7.50988
56 4ORM 2V6 0.03204 0.42594 7.81759
57 4ORM FMN 0.03204 0.42594 7.81759
58 4ORM ORO 0.03204 0.42594 7.81759
59 2C6Q NDP 0.04285 0.40653 7.81759
60 1MJH ATP 0.01966 0.40104 8.02469
61 4CW5 FMN 0.0103 0.41125 8.14332
62 4MO2 FAD 0.0467 0.40109 8.46906
63 1M5W DXP 0.0161 0.40001 9.46502
64 2ZRU FMN 0.008001 0.43908 10.0977
65 3TAO PGH 0.003009 0.42559 10.1124
66 4WEI GLC GAL 0.007594 0.41551 10.8303
67 1AKV FMN 0.02383 0.40001 11.5646
68 4BI7 PGA 0.02893 0.40247 12.8405
69 3HGM ATP 0.01728 0.40379 13.6054
70 2B4G FMN 0.01018 0.42276 13.6808
71 2BTM PGA 0.001703 0.44246 20.6349
72 1SW0 PGA 0.002996 0.42824 25.4032
Pocket No.: 2; Query (leader) PDB : 3N9R; Ligand: TD3; 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: 3n9r.bio3) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3N9R; Ligand: TD3; Similar sites found: 19
This union binding pocket(no: 3) in the query (biounit: 3n9r.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5X40 ACP 0.02171 0.40444 1.0274
2 4JLS 3ZE 0.007176 0.41848 1.97368
3 5GXU FMN 0.006611 0.42516 2.28013
4 1LYX PGA 0.0007506 0.43203 2.82258
5 3IES M24 0.02425 0.41595 2.9316
6 1G6H ADP 0.01049 0.40665 3.11284
7 5DWQ SFG 0.01977 0.40651 3.58306
8 3NTD COA 0.0447 0.40078 3.90879
9 5NB7 8NQ 0.02568 0.40074 4.34783
10 3F81 STT 0.009153 0.41644 4.37158
11 1QDS PGA 0.0008451 0.44601 5.17928
12 2WHX ADP 0.009125 0.41263 5.21173
13 5M3E APR 0.02237 0.40951 5.45455
14 1TLG GAL 0.002291 0.43881 5.6
15 4NAE 1GP 0.002133 0.44096 7.55556
16 2ZX2 RAM 0.01438 0.40134 7.69231
17 4JEJ 1GP 0.001688 0.42351 8.19672
18 3QPB URA 0.002618 0.43947 9.44625
19 3KC1 2T6 0.02099 0.40021 16.3205
Pocket No.: 4; Query (leader) PDB : 3N9R; Ligand: TD3; Similar sites found: 8
This union binding pocket(no: 4) in the query (biounit: 3n9r.bio2) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2CDU FAD 0.02555 0.41295 1.62866
2 1I9G SAM 0.02023 0.40043 2.5
3 1KQF MGD 0.03662 0.40278 8.79479
4 5IXJ THR 0.04143 0.40384 10.4235
5 3PA8 621 0.01572 0.40051 11.0236
6 1DIG NAP 0.02361 0.41049 11.7647
7 3RYC GTP 0.03458 0.40085 13.2867
8 5JAQ NAI 0.04979 0.4005 15.6352
Pocket No.: 5; Query (leader) PDB : 3N9R; Ligand: TD3; Similar sites found: 8
This union binding pocket(no: 5) in the query (biounit: 3n9r.bio4) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5AHW CMP 0.01419 0.40066 1.36054
2 1F74 NAY 0.04629 0.40037 2.38908
3 2YVF FAD 0.0382 0.42053 2.9316
4 2YVF NAD 0.03917 0.42053 2.9316
5 5EYP GDP 0.02916 0.40106 3.5503
6 2FMD MAN MAN 0.01747 0.40307 3.75
7 1MO9 FAD 0.008449 0.46585 3.90879
8 5F7U GLC GLC 0.01428 0.40092 6.18893
Pocket No.: 6; Query (leader) PDB : 3N9R; Ligand: TD3; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 3n9r.bio4) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Feedback