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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 13 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 with APoc: 171
This union binding pocket(no: 1) in the query (biounit: 3n9r.bio3) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 4JNA FAD 1.62866
2 2Z6I FMN 1.9544
3 2FK8 SAM 1.9544
4 5HSA FAS 1.9544
5 4HKP TKW 1.9544
6 6BKA FMN 1.9544
7 1CT9 AMP 1.9544
8 4JLS 3ZE 1.97368
9 1TPY SAH 2.09059
10 4Q4K FMN 2.28013
11 5GVH FMN 2.28013
12 4XP7 FNR 2.28013
13 1RHC F42 ACN 2.28013
14 2QCD U5P 2.30769
15 5A5W GUO 2.37154
16 1L1E SAH 2.43902
17 1P4A PCP 2.45614
18 5XKT GNP 2.5
19 3NTY 5P3 2.60586
20 3NTY NAP 2.60586
21 1RPN NDP 2.60586
22 4RGQ 13P 2.60586
23 1JJ7 ADP 2.69231
24 1LYX PGA 2.82258
25 4EHU ANP 2.89855
26 2GJN NIS 2.9316
27 2GJN FMN 2.9316
28 1OVD ORO 2.9316
29 5EXW 7DT 2.9316
30 1OVD FMN 2.9316
31 4HA6 FAD 2.9316
32 6F97 FAD 2.9316
33 3OIX FMN 2.9316
34 1CZR FMN 2.95858
35 4WZ6 ATP 3.10345
36 1G6H ADP 3.11284
37 1KPG SAH 3.13589
38 4Z87 5GP 3.25733
39 5VN0 NAI 3.25733
40 5VN0 FAD 3.25733
41 1LQA NDP 3.25733
42 4Z0G 5GP 3.25733
43 1Z2I NAD 3.25733
44 4GA6 AMP 3.25733
45 2CWH NDP 3.25733
46 1PZ1 NAP 3.25733
47 5X68 FAD 3.25733
48 4HE2 AMP 3.25733
49 5CSS G3P 3.58306
50 1GTE FMN 3.58306
51 1GTE IUR 3.58306
52 1UUO FMN 3.58306
53 1UUO BRF 3.58306
54 1UUO ORO 3.58306
55 4IGH FMN 3.58306
56 4IGH 1EA 3.58306
57 4IGH ORO 3.58306
58 3MJY FMN 3.58306
59 3MJY IJZ 3.58306
60 3NTA COA 3.58306
61 5DX1 SFG 3.58306
62 5J5R 6G1 3.59897
63 5J5R IMP 3.59897
64 4H2D FMN 3.63636
65 3B5J 12D 3.7037
66 3JZB 4HY 3.74532
67 1MVQ MMA 3.81356
68 1N46 PFA 3.87597
69 3H7R NAP 3.90879
70 2V58 LZJ 3.90879
71 2RCU BUJ 3.90879
72 3NTD COA 3.90879
73 2PZE ATP 3.93013
74 4YMZ 13P 3.98406
75 4WOH 4NP 4.21687
76 5OCG GNP 4.2328
77 3FG2 FAD 4.23453
78 4IXH IMP 4.23453
79 1LVK MNT BEF 4.23453
80 1D4D FAD 4.23453
81 5X7Q GLC GLC 4.23453
82 2Q8Z NUP 4.23453
83 2WC1 FMN 4.3956
84 1LBF 137 4.45344
85 3BW2 FMN 4.56026
86 2BUP ADP 4.56026
87 2BUP ATP 4.56026
88 3FJO FMN 4.56026
89 5EYW PGA 4.81928
90 4M3P HCS 4.88599
91 3LXD FAD 4.88599
92 4NZ6 DLY 4.88599
93 1QDS PGA 5.17928
94 2WHX ADP 5.21173
95 2AWN ADP 5.21173
96 1O94 AMP 5.21173
97 2Y88 2ER 5.32787
98 3BXF 13P 5.4902
99 3BXF FBP 5.4902
100 1YB5 NAP 5.53746
101 3CV6 HXS 5.53746
102 3CV6 NAP 5.53746
103 3OVR 5SP 5.70175
104 5FYR INS 5.7047
105 6BVE PGA 5.71429
106 1ME8 RVP 5.86319
107 1PVN MZP 5.86319
108 1NAA 6FA 5.86319
109 5EOU ATP 5.86319
110 2BLE 5GP 5.99455
111 2YPI PGA 6.07287
112 1YQT ADP 6.18893
113 5YV5 ADP 6.18893
114 5EB4 FAD 6.18893
115 1JI0 ATP 6.25
116 1DQX BMP 6.36704
117 1TRD PGH 6.4
118 2Z6J FMN 6.51466
119 1OX5 1PR 6.51466
120 5FBK TCR 6.51466
121 3QVP FAD 6.51466
122 1AG9 FMN 6.85714
123 1OBV FMN 7.10059
124 5AHN IMP 7.36196
125 3NHB ADP 7.49186
126 4EWN 0VR 7.50988
127 4NAE 1GP 7.55556
128 2ZX2 RAM 7.69231
129 5M45 AMP 7.7381
130 4ORM ORO 7.81759
131 4ORM 2V6 7.81759
132 4ORM FMN 7.81759
133 2C6Q NDP 7.81759
134 2C6Q IMP 7.81759
135 1MJH ATP 8.02469
136 3VET CP 8.14332
137 3VET ADP 8.14332
138 4CW5 FMN 8.14332
139 4JEJ 1GP 8.19672
140 2HF9 GSP 8.40708
141 4MO2 FAD 8.46906
142 4Z24 FAD 8.79479
143 3GD4 FAD 9.12052
144 1KPH SAH 9.40767
145 3QPB URA 9.44625
146 1M5W DXP 9.46502
147 1FQJ ALF 9.52381
148 6GAS FAD 9.77199
149 2FLI DX5 10
150 2ZRU FMN 10.0977
151 3TAO PGH 10.1124
152 2ZFZ ARG 10.1266
153 1T57 FMN 10.6796
154 5AHM IMP 10.7492
155 4WEI GLC GAL 10.8303
156 3PA8 621 11.0236
157 4AF0 IMP 11.4007
158 1AKV FMN 11.5646
159 4WZH FMN 12.0521
160 4BI7 PGA 12.8405
161 3C3N FMN 13.0293
162 5K9B FMN 13.3333
163 1CX9 NHP 13.355
164 3HGM ATP 13.6054
165 5XFV FMN 13.6808
166 3FGC FMN 16.6124
167 2GKS ADP 20.1954
168 2BTM PGA 20.6349
169 5BVA FAD 22.8013
170 1KBJ FMN 25.0814
171 1SW0 PGA 25.4032
Pocket No.: 2; Query (leader) PDB : 3N9R; Ligand: TD3; Similar sites found with APoc: 42
This union binding pocket(no: 2) in the query (biounit: 3n9r.bio3) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 5GSN FAD 1.62866
2 4DDY DN6 1.90114
3 5GVL PLG 1.9544
4 5GVL GI8 1.9544
5 5GXU FMN 2.28013
6 1I9G SAM 2.5
7 6BWL NAD 2.60586
8 3FPF MTA 2.68456
9 3FPF TNA 2.68456
10 4BLW SAH 2.76817
11 3IES M24 2.9316
12 3CTY FAD 3.25733
13 4P5E N6P 3.28947
14 5EYP GDP 3.5503
15 5DX0 SFG 3.58306
16 5DXA SFG 3.58306
17 5DX8 SFG 3.58306
18 5DWQ SFG 3.58306
19 2FMD MAN MAN 3.75
20 1MO9 KPC 3.90879
21 3F81 STT 4.37158
22 6FA4 D1W 4.62428
23 1QXO FMN 4.88599
24 2GZ3 NAP 5.53746
25 1TLG GAL 5.6
26 2YYY NAP 5.86319
27 4OXX FMN 6.17284
28 5F7U GLC GLC 6.18893
29 3N39 FMN 7.18954
30 1KOR ANP 7.49186
31 1KOR ARG 7.49186
32 1KOR SIN 7.49186
33 1KQF MGD 8.79479
34 1TE2 PGA 8.84956
35 1EJ0 SAM 9.44444
36 2RHQ GAX 9.44625
37 2PWY SAH 9.68992
38 6AMI TRP 10.4235
39 6AM8 PLT 10.4235
40 3A4T SFG 10.5839
41 3AB1 FAD 11.0749
42 5JAQ NAI 15.6352
Pocket No.: 3; Query (leader) PDB : 3N9R; Ligand: TD3; Similar sites found with APoc: 59
This union binding pocket(no: 3) in the query (biounit: 3n9r.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 5X40 ACP 1.0274
2 2CDU FAD 1.62866
3 2Q8M AMP 1.9544
4 4IP7 FBP 1.9544
5 3MAG SAH 1.9544
6 3MCT SAH 2.0202
7 5FUB SAH 2.28013
8 1X87 NAD 2.28013
9 2VZZ SCA 2.29358
10 4K38 SAM 2.60586
11 4B2D FBP 2.60586
12 1B1C FMN 2.76243
13 5H4S RAM 2.8169
14 2YVF FAD 2.9316
15 2YVF NAD 2.9316
16 2RGO FAD 2.9316
17 3E1T FAD 2.9316
18 3GFZ C2E 2.9316
19 5Z6T NAP 2.9316
20 1VP5 NAP 3.02013
21 6CI9 NAP 3.0888
22 2GMH FAD 3.25733
23 2OQ2 A3P 3.44828
24 2WET FAD 3.58306
25 4PIV NDP 3.93939
26 5LJI FMN 4.05405
27 6AIN FAD 4.23453
28 1U7Z PMT 4.42478
29 3WDM ADN 4.5977
30 2C7G ODP 5.21173
31 1DJN FMN 5.21173
32 1LOR BMP 5.26316
33 5M3E APR 5.45455
34 2HJR CIT 5.53746
35 4MP8 MLI 5.86319
36 4MP8 NAD 5.86319
37 5MB4 NAG 6.18893
38 1RM6 FAD 7.16612
39 2D1S SLU 7.49186
40 3VET TOY 8.14332
41 3GFB NAD 8.14332
42 6GNA FAD 8.33333
43 1XHC FAD 9.12052
44 1TV5 FMN 9.48081
45 3HVJ 705 9.50226
46 5WS9 AMP 10.4235
47 5EIB GTP 11.2426
48 3WV8 ATP 11.4679
49 1DIG NAP 11.7647
50 1GPE FAD 12.7036
51 6ASY ATP 12.7036
52 3RYC GTP 13.2867
53 6EBQ FMN 13.75
54 5KK4 44E 14.5833
55 4LNU GTP 14.658
56 3KC1 2T6 16.3205
57 6B8B ADP 23.2932
58 1E6E FAD 25.7812
59 3QF7 ANP 34
Pocket No.: 4; Query (leader) PDB : 3N9R; Ligand: TD3; Similar sites found with APoc: 5
This union binding pocket(no: 4) in the query (biounit: 3n9r.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 1ZOS MTM 1.30435
2 5AHW CMP 1.36054
3 2CWH PYC 3.25733
4 5VEG FMN 3.93258
5 1FEC FAD 9.77199
Pocket No.: 5; Query (leader) PDB : 3N9R; Ligand: TD3; Similar sites found with APoc: 3
This union binding pocket(no: 5) in the query (biounit: 3n9r.bio4) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 1MO9 FAD 3.90879
2 1O94 ADP 5.21173
3 2JJK R15 16.2722
Pocket No.: 6; Query (leader) PDB : 3N9R; Ligand: TD3; Similar sites found with APoc: 50
This union binding pocket(no: 6) in the query (biounit: 3n9r.bio4) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 1L2T ATP 1.70213
2 4HKP 16B 1.9544
3 3C8F MT2 2.04082
4 3MI2 PFU 2.15054
5 5VSM MET 2.28013
6 5VSM 5AD 2.28013
7 2P3V SRT 2.34375
8 1UJP CIT 2.58303
9 5G41 AP5 2.69058
10 2PLK P3D 2.86396
11 5ZXD ATP 2.9316
12 5VC5 96M 3.11419
13 1YY5 FAD 3.25733
14 4OHY ANP 3.90879
15 1Q6O LG6 4.16667
16 4L2I NAD 4.18251
17 4L2I FAD 4.18251
18 1FFU CDP 4.52962
19 2NVA PL2 4.56026
20 5GJO PLP 4.56026
21 4RLQ 3SK 4.56026
22 1X1Z BMP 4.7619
23 2IXE ATP 4.79705
24 1TUF AZ1 5.21173
25 1DJN ADP 5.21173
26 1OFD FMN 5.21173
27 1OFD AKG 5.21173
28 1RDL MMA 5.30973
29 1B0U ATP 5.34351
30 1DBT U5P 5.43933
31 2HXW FLC 5.48523
32 5T9C G3P 5.97015
33 5H68 AGS 6.18893
34 2OFW ADX 6.25
35 4KQI NIO 6.51466
36 3RLF ANP 6.51466
37 5VHC BEF ADP 6.51466
38 4YMU ATP 7.27273
39 1F2U ATP 7.43243
40 2OO0 PLP 7.81759
41 5L3R GCP 8.87372
42 3QH2 3NM 9.04977
43 1OXV ANP 9.44625
44 6C2Z P1T 10.0977
45 5L3S GNP 12.0805
46 5AWQ GLC GLC 12.3779
47 5WGG SAM 12.7036
48 4NJH SAM 14.3478
49 4NJH 2K8 14.3478
50 3EXS 5RP 14.9321
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