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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 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
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 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 (12)
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 5VJF - 13P C3 H7 O6 P C(C(=O)COP....
6 3N9S Ki = 0.07 uM TD4 C6 H15 N O10 P2 C(CCOP(=O)....
7 5UD2 - 13P C3 H7 O6 P C(C(=O)COP....
8 5UD4 - P6T C6 H14 O12 P2 C([C@H]([C....
9 5UCP - G3H C3 H7 O6 P C([C@H](C=....
10 5UD3 - P6F C6 H14 O12 P2 C([C@H]([C....
11 3C56 Ki = 0.013 uM PH4 C5 H13 N O10 P2 C(CN(C(=O)....
12 5UCZ - 13P C3 H7 O6 P C(C(=O)COP....
70% Homology Family (12)
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 5VJF - 13P C3 H7 O6 P C(C(=O)COP....
6 3N9S Ki = 0.07 uM TD4 C6 H15 N O10 P2 C(CCOP(=O)....
7 5UD2 - 13P C3 H7 O6 P C(C(=O)COP....
8 5UD4 - P6T C6 H14 O12 P2 C([C@H]([C....
9 5UCP - G3H C3 H7 O6 P C([C@H](C=....
10 5UD3 - P6F C6 H14 O12 P2 C([C@H]([C....
11 3C56 Ki = 0.013 uM PH4 C5 H13 N O10 P2 C(CN(C(=O)....
12 5UCZ - 13P C3 H7 O6 P C(C(=O)COP....
50% Homology Family (19)
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 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 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....
14 2ISW Ki = 37 nM PGH C2 H6 N O6 P C(C(=O)NO)....
15 3GAY Kd = 20 nM P6T C6 H14 O12 P2 C([C@H]([C....
16 3OHI Ki = 14 uM HDX C8 H13 N O9 P2 C1=CN(C(=O....
17 3GB6 - P6F C6 H14 O12 P2 C([C@H]([C....
18 2ISV Ki = 37 nM PGH C2 H6 N O6 P C(C(=O)NO)....
19 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 with APoc: 112
This union binding pocket(no: 1) in the query (biounit: 3c56.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 1I7A FLC None
2 2G77 AF3 1.62866
3 2Q8M AMP 1.9544
4 2Z6I FMN 1.9544
5 6BKA FMN 1.9544
6 4HKP TKW 1.9544
7 4IP7 FLC 1.9544
8 4JLS 3ZE 1.97368
9 3C8F MT2 2.04082
10 4Q4K FMN 2.28013
11 2JK0 ASP 2.28013
12 2Z48 A2G 2.28013
13 3GDN FAD 2.28013
14 3GDN HBX 2.28013
15 5GVH FMN 2.28013
16 5A5W GUO 2.37154
17 1UJP CIT 2.58303
18 1LYX PGA 2.82258
19 2GJN FMN 2.9316
20 2GJN NIS 2.9316
21 1OVD ORO 2.9316
22 1OVD FMN 2.9316
23 4I9B 1KA 2.9316
24 4WZ6 ATP 3.10345
25 1J3R 6PG 3.15789
26 2D2F ADP 3.2
27 2OMN IPH 3.22581
28 4HE2 AMP 3.25733
29 1YKJ FAD 3.25733
30 1YKJ PHB 3.25733
31 3R7F CP 3.28947
32 3WW2 SF9 3.51562
33 4K91 SIN 3.58306
34 5LTJ ADP 3.58306
35 5CSS G3P 3.58306
36 3B5J 12D 3.7037
37 2FMD MAN MAN 3.75
38 1MVQ MMA 3.81356
39 2PZE ATP 3.93013
40 4YMZ 13P 3.98406
41 1CY2 TMP 4.23453
42 2Q8Z NUP 4.23453
43 1LVK MNT BEF 4.23453
44 3BW2 FMN 4.56026
45 4RLQ 3SK 4.56026
46 6FA4 D1W 4.62428
47 5EYW PGA 4.81928
48 4M3P HCS 4.88599
49 2OG2 MLI 4.88599
50 3ENG CBI 5.16432
51 1QDS PGA 5.17928
52 2WHX ADP 5.21173
53 1OFD FMN 5.21173
54 1OFD AKG 5.21173
55 2Y88 2ER 5.32787
56 1B0U ATP 5.34351
57 3OVR 5SP 5.70175
58 6BVE PGA 5.71429
59 2G30 ALA ALA PHE 5.81395
60 3QIN P1Y 6
61 2YPI PGA 6.07287
62 1UYY BGC BGC 6.10687
63 3EYK EYK 6.18893
64 1YQT ADP 6.18893
65 4WOE ADP 6.18893
66 5F7U GLC GLC 6.18893
67 1JI0 ATP 6.25
68 1TRD PGH 6.4
69 3GE7 AFQ 6.51466
70 2Z6J FMN 6.51466
71 5FBK TCR 6.51466
72 1PVC ILE SER GLU VAL 7.35294
73 5AHN IMP 7.36196
74 3NHB ADP 7.49186
75 4EWN 0VR 7.50988
76 4NAE 1GP 7.55556
77 4ORM FMN 7.81759
78 4ORM 2V6 7.81759
79 4ORM ORO 7.81759
80 5C9J DAO 7.82918
81 6CEP OXM 8.14332
82 4JEJ 1GP 8.19672
83 2YMZ LAT 8.46154
84 4KCT PYR 8.46906
85 4JZ8 CIT 8.79479
86 3TW1 AHN 8.86076
87 3QH2 3NM 9.04977
88 3QPB URA 9.44625
89 1OXV ANP 9.44625
90 1M5W DXP 9.46502
91 2FLI DX5 10
92 2ZRU FMN 10.0977
93 3TAO PGH 10.1124
94 2ZFZ ARG 10.1266
95 6AM8 TRP 10.4235
96 6CZY PMP 10.4235
97 4CZ1 VNJ 10.5263
98 2AK3 AMP 12.3894
99 4BI7 PGA 12.8405
100 3C3N FMN 13.0293
101 4P86 5GP 13.1148
102 1CX9 NHP 13.355
103 5XFV FMN 13.6808
104 3A4M ADP 14.2308
105 5KK4 44E 14.5833
106 2BTM PGA 20.6349
107 3IWD M2T 24.1935
108 2XI7 XI7 24.4565
109 1KBJ FMN 25.0814
110 1KBI FMN 25.0814
111 1SW0 PGA 25.4032
112 43CA NPO 26.4957
Pocket No.: 2; Query (leader) PDB : 3C56; Ligand: PH4; Similar sites found with APoc: 31
This union binding pocket(no: 2) in the query (biounit: 3c56.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 2ZZV LAC 1.9544
2 4WQQ MAN 2.12766
3 4XFR CIT 2.60586
4 5ZXD ATP 2.9316
5 2GMH FAD 3.25733
6 3VM7 GLC 3.25733
7 5KOX FAD 3.58306
8 5NE2 DGL 3.58306
9 1GTE FMN 3.58306
10 1GTE IUR 3.58306
11 1GET NAP 3.58306
12 1GET FAD 3.58306
13 4PIV NDP 3.93939
14 1P19 IMP 4.0724
15 4WOH 4NP 4.21687
16 1ZPD CIT 4.56026
17 6AR9 3L4 5.51471
18 4TQK NAG 5.53746
19 5T9C G3P 5.97015
20 5YV5 ADP 6.18893
21 4UP4 GAL NAG 6.18893
22 4KQI NIO 6.51466
23 4KQI RBZ 6.51466
24 2ZX2 RAM 7.69231
25 3VET ADP 8.14332
26 3VET TOY 8.14332
27 3VET CP 8.14332
28 4WEI GLC GAL 10.8303
29 2HK9 SKM 10.9091
30 4AF0 MOA 11.4007
31 1KBI PYR 25.0814
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