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Receptor
PDB id Resolution Class Description Source Keywords
3WQM 2.1 Å EC: 3.1.7.8_3.1.7.9 CRYSTAL STRUCTURE OF RV3378C WITH INHIBITOR BPH-629 MYCOBACTERIUM TUBERCULOSIS DITERPENE SYNTHASE HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: STRUCTURE AND INHIBITION OF TUBERCULOSINOL SYNTHASE DECAPRENYL DIPHOSPHATE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS. J.AM.CHEM.SOC. V. 136 2892 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PO4 A:405;
A:404;
Invalid;
Invalid;
none;
none;
submit data
94.971 O4 P [O-]P...
B29 A:401;
A:402;
Valid;
Valid;
none;
none;
Kd = 560 nM
448.3 C20 H18 O8 P2 c1ccc...
MG A:403;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3WQM 2.1 Å EC: 3.1.7.8_3.1.7.9 CRYSTAL STRUCTURE OF RV3378C WITH INHIBITOR BPH-629 MYCOBACTERIUM TUBERCULOSIS DITERPENE SYNTHASE HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: STRUCTURE AND INHIBITION OF TUBERCULOSINOL SYNTHASE DECAPRENYL DIPHOSPHATE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS. J.AM.CHEM.SOC. V. 136 2892 2014
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4KT8 - TIP n/a n/a
2 3WQM Kd = 560 nM B29 C20 H18 O8 P2 c1ccc2c(c1....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4KT8 - TIP n/a n/a
2 3WQM Kd = 560 nM B29 C20 H18 O8 P2 c1ccc2c(c1....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4KT8 - TIP n/a n/a
2 3WQM Kd = 560 nM B29 C20 H18 O8 P2 c1ccc2c(c1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: B29; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 B29 1 1
2 B08 0.402597 0.829268
3 B28 0.402597 0.829268
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3WQM; Ligand: B29; Similar sites found with APoc: 189
This union binding pocket(no: 1) in the query (biounit: 3wqm.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 5NNT DPV None
2 2VWA PTY None
3 4F4S EFO None
4 4V1F BQ1 None
5 2VBQ BSJ None
6 1HBK MYR None
7 1L0I PSR None
8 4WG0 CHD None
9 3ZQE DXC 0.664452
10 2E2R 2OH 0.819672
11 4I90 CHT 1.3289
12 4B1V LAB 1.3289
13 3D9F N6C 1.3289
14 3D9F FAD 1.3289
15 3SJH LAR 1.3289
16 5B0W 22B 1.37457
17 4ETZ C2E 1.6835
18 5UGW GSH 1.71429
19 3KMZ EQO 1.8797
20 5XVH TLA 1.99336
21 3AQT RCO 2.04082
22 5XK9 DMA 2.15517
23 5XK9 GST 2.15517
24 1JGS SAL 2.17391
25 5A1S FLC 2.32558
26 2HZL PYR 2.32558
27 3V66 D3A 2.32558
28 3ZS7 ATP 2.33333
29 4WGF HX2 2.43902
30 1DTL BEP 2.48447
31 4O4Z N2O 2.5974
32 1KHT AMP 2.60417
33 4OIV XX9 2.65487
34 4RW3 TDA 2.65781
35 2UW1 GVM 2.65781
36 5GVL GI8 2.65781
37 5GVL PLG 2.65781
38 1KY8 NAP 2.65781
39 5FPN KYD 2.65781
40 3HX3 RET 2.65781
41 4EI7 GDP 2.65781
42 3T3Z 9PL 2.65781
43 2WOX NDP 2.65781
44 1PZO CBT 2.6616
45 1GEG GLC 2.73438
46 2P3V SRT 2.73438
47 1WMA AB3 2.89855
48 4ZVV NAD 2.99003
49 4ZVV GN0 2.99003
50 3B9Z CO2 2.99003
51 6H8S FSZ 2.99003
52 3GDN MXN 2.99003
53 4ARE FLC 2.99003
54 4M51 BEZ 2.99003
55 5A0U CHT 2.99003
56 4UCC ZKW 3.00429
57 1NU4 MLA 3.09278
58 2GBB CIT 3.20513
59 1NHZ 486 3.21429
60 4YC9 4C1 3.26087
61 4LY9 1YY 3.32226
62 4LY9 S6P 3.32226
63 3NBK PNS 3.38983
64 5ZRR 9J3 3.39623
65 1M2Z BOG 3.50195
66 2AX9 BHM 3.51562
67 4P6X HCY 3.52941
68 1ZPD CIT 3.65448
69 5IM3 DTP 3.65448
70 1RDT L79 3.71901
71 1VKF CIT 3.7234
72 3FAL REA 3.7594
73 3TL1 JRO 3.77358
74 1FM9 9CR 3.78151
75 6A5Y 9CR 3.78151
76 5N26 CPT 3.84615
77 1DKF OLA 3.86266
78 4M8E 29V 3.8961
79 4POJ 2VP 3.8961
80 5M37 9SZ 3.91304
81 5M36 9SZ 3.93013
82 3H0A 9RA 3.94737
83 5OLK DTP 3.98671
84 4K10 NI9 3.98671
85 4RQL SNE 3.98671
86 6B5G CQY 3.98671
87 6B5G NAD 3.98671
88 3CEV ARG 4.01338
89 1YRO UDP 4.06504
90 5HC8 61G 4.21456
91 3GCM 5GP 4.31894
92 5MTE BB2 4.37956
93 1SBR VIB 4.5
94 5N18 8HZ 4.58716
95 5NTP 98E 4.62185
96 3SFI 3SF 4.66102
97 2I0G I0G 4.66926
98 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 4.78261
99 5D9J 0N8 4.81283
100 5K7K 6RJ 4.8218
101 5IXK 6EW 4.82456
102 3FXU TSU 4.91803
103 4ZGM 32M 4.91803
104 5NWI TYR PHE SER SEP ASN 4.96183
105 5W7B MYR 4.96454
106 5LX9 OLB 4.98339
107 6CGN DA 4.98339
108 4NTX AMR 5.04202
109 1TZD ADP 5.09091
110 3B6C SDN 5.12821
111 1ZED PNP 5.31561
112 5CX6 CDP 5.31561
113 4URX FK1 5.31561
114 1RL4 BL5 5.31915
115 5V3Y 5V8 5.59441
116 4L2I FAD 5.64784
117 1FCH TYR GLN SER LYS LEU 5.64784
118 4NTO 1PW 5.7971
119 6CB2 OLC 5.80205
120 5CHR 4NC 5.83942
121 3ND6 ATP 5.84795
122 3Q8G PEE 5.98007
123 3NHT U46 6.08108
124 3WDM ADN 6.13027
125 3PVT 3HC 6.17761
126 3N7S 3N7 6.25
127 5UC1 486 6.30631
128 4A4Z ANP 6.31229
129 1MID LAP 6.59341
130 2YPO PHE 6.64452
131 3SE5 ANP 6.70732
132 4F4P 0SB 6.95971
133 4DXJ 0M9 6.97674
134 4MGA 27L 7.05882
135 2BJ4 OHT 7.14286
136 5MWE TCE 7.14286
137 4TV1 36M 7.17131
138 3MBG FAD 7.19424
139 2FP2 TSA 7.22892
140 5NM7 GLY 7.5188
141 5AAV GW5 7.53968
142 2QE4 JJ3 7.66129
143 2WOR 2AN 8
144 4EN4 GT1 8.30565
145 4EN4 ATP 8.30565
146 4EN4 GT0 8.30565
147 5DCH 1YO 8.33333
148 5EK3 5PK 8.63787
149 5TVI MYR 8.69565
150 6HL8 GUA 9.30233
151 3PE2 E1B 9.30233
152 5V13 JH3 9.375
153 3F8C HT1 9.52381
154 2BCG GER 9.63455
155 4BNU 9KQ 9.63455
156 4Q9M FPP 9.7561
157 5V4R MGT 9.87654
158 5XJ7 87O 9.95025
159 5XJ8 NKO 9.95025
160 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 9.96678
161 3E85 BSU 10.1266
162 4INB 1F6 10.274
163 2OBD 2OB 10.9635
164 2OBD PCW 10.9635
165 3G08 FEE 11.1111
166 4U82 FPS 11.3281
167 5F74 AMP 11.3821
168 2VG1 FPP 11.4035
169 1SR7 MOF 11.583
170 4OAR 2S0 11.6279
171 4NAT ADP 11.875
172 4NAT 2W5 11.875
173 3KXC PLM 12.0253
174 5OCA 9QZ 12.6984
175 1T0S BML 13.9535
176 6CHP F0Y 14.9068
177 1U72 NDP 15.0538
178 1U72 MTX 15.0538
179 4OGQ 7PH 16.2162
180 4OGQ 1O2 16.2162
181 2X5W K2B 16.6113
182 6GH1 ARG LEU PRO ALA LYS ALA PRO LEU LEU 17
183 5U98 1KX 17.1717
184 5W97 CHD 17.3913
185 5Z84 CHD 17.3913
186 5ZCO CHD 17.3913
187 2XRH NIO 20
188 2Y69 CHD 22.5
189 3WYJ H78 23.7154
Pocket No.: 2; Query (leader) PDB : 3WQM; Ligand: B29; 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: 3wqm.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3WQM; Ligand: B29; Similar sites found with APoc: 62
This union binding pocket(no: 3) in the query (biounit: 3wqm.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 1NLI ADE 2.01613
2 1LAF ARG 2.10084
3 2Z7I 742 2.32558
4 2FZH DH1 2.42718
5 1YQZ FAD 2.65781
6 1YOK P6L 2.73438
7 4KM2 ATR 2.7933
8 4KM2 TOP 2.7933
9 1ZDU P3A 2.85714
10 3KJS DQ1 2.99003
11 5XQL C2E 3.09278
12 4G86 BNT 3.16901
13 5W6Y TRP 3.32226
14 1D8C GLV 3.32226
15 4EIL NDP 3.32226
16 3BD9 A3P 3.57143
17 1ZRH A3P 3.64964
18 2GZ3 NAP 3.65448
19 2NUN ADP 3.65448
20 3ZCN ATP 3.65448
21 6CS8 F9Y 3.65448
22 2BO4 FLC 3.65448
23 1RDT 570 3.71901
24 5A4W QCT 3.77358
25 1VKJ A3P 3.85965
26 4WBD CIT 3.98671
27 4ONC 40B 4.22535
28 2OG2 MLI 4.31894
29 3B9Q MLI 4.98339
30 2VOH CIT 5.09554
31 3ZC7 ATP 5.11811
32 1T8U UAP SGN IDS SGN 5.14706
33 1T8U A3P 5.14706
34 5B0I BOG 5.24781
35 4DP3 NDP 5.31561
36 4DP3 MMV 5.31561
37 1NST A3P 5.31561
38 2ZCQ B65 5.80205
39 3ZLM ANP 5.85106
40 3NOJ PYR 5.88235
41 2J5V PCA 5.98007
42 3ZCB ATP 6.56566
43 3RYC GTP 6.64452
44 1Q19 SSC 6.64452
45 2DPY ADP 6.64452
46 2OBM ADP 6.97674
47 3EEL 53T 7.04846
48 4U0S ADP 7.97342
49 3RUV ANP 8.63787
50 6C0B MLI 8.9701
51 5E5U MLI 9.04523
52 3CYI ATP 9.09091
53 1GXU 2HP 9.89011
54 5URY PAM 10.274
55 4LAE NAP 11.976
56 4LAE 1VM 11.976
57 5A96 GTP 12.4498
58 1AOE GW3 12.5
59 1AOE NDP 12.5
60 4KVL PLM 13.9535
61 4YV5 SVR 22.1311
62 3KPE TM3 38.4615
Pocket No.: 4; Query (leader) PDB : 3WQM; Ligand: B29; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 3wqm.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
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