Receptor
PDB id Resolution Class Description Source Keywords
3WYJ 2.1 Å EC: 2.5.1.31 STRUCTURE OF E. COLI UNDECAPRENYL DIPHOSPHATE SYNTHASE IN CO BPH-789 ESCHERICHIA COLI K-12 TRANSFERASE
Ref.: ANTIBACTERIAL DRUG LEADS: DNA AND ENZYME MULTITARGE J.MED.CHEM. 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
H78 A:900;
Valid;
none;
ic50 = 1.9 uM
948.677 C34 H36 N2 O18 P4 S2 c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3WYJ 2.1 Å EC: 2.5.1.31 STRUCTURE OF E. COLI UNDECAPRENYL DIPHOSPHATE SYNTHASE IN CO BPH-789 ESCHERICHIA COLI K-12 TRANSFERASE
Ref.: ANTIBACTERIAL DRUG LEADS: DNA AND ENZYME MULTITARGE J.MED.CHEM. 2015
Members (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2E9D - B76 C20 H20 O8 P2 c1ccc(cc1)....
2 1X09 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
3 3TH8 - TH9 C19 H27 N O5 CCCCCCOc1c....
4 5CQJ ic50 = 7.5 uM 53Q C21 H17 Cl O COc1ccc(cc....
5 1V7U - FPP C15 H28 O7 P2 CC(=CCC/C(....
6 2E9C - B75 C24 H23 N O9 P2 S c1ccc2cc(c....
7 2E9A - B28 C20 H20 O7 P2 c1ccc(cc1)....
8 1X06 - FPS C15 H28 O6 P2 S CC(=CCC/C(....
9 1X07 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
10 2E98 - B29 C20 H18 O8 P2 c1ccc2c(c1....
11 3WYJ ic50 = 1.9 uM H78 C34 H36 N2 O18 P4 S2 c1cc(cc(c1....
12 1X08 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
13 2E99 - B08 C20 H20 O7 P2 c1ccc(cc1)....
70% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2E9D - B76 C20 H20 O8 P2 c1ccc(cc1)....
2 1X09 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
3 3TH8 - TH9 C19 H27 N O5 CCCCCCOc1c....
4 5CQJ ic50 = 7.5 uM 53Q C21 H17 Cl O COc1ccc(cc....
5 1V7U - FPP C15 H28 O7 P2 CC(=CCC/C(....
6 2E9C - B75 C24 H23 N O9 P2 S c1ccc2cc(c....
7 2E9A - B28 C20 H20 O7 P2 c1ccc(cc1)....
8 1X06 - FPS C15 H28 O6 P2 S CC(=CCC/C(....
9 1X07 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
10 2E98 - B29 C20 H18 O8 P2 c1ccc2c(c1....
11 3WYJ ic50 = 1.9 uM H78 C34 H36 N2 O18 P4 S2 c1cc(cc(c1....
12 1X08 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
13 2E99 - B08 C20 H20 O7 P2 c1ccc(cc1)....
50% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2E9D - B76 C20 H20 O8 P2 c1ccc(cc1)....
2 1X09 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
3 3TH8 - TH9 C19 H27 N O5 CCCCCCOc1c....
4 5CQJ ic50 = 7.5 uM 53Q C21 H17 Cl O COc1ccc(cc....
5 1V7U - FPP C15 H28 O7 P2 CC(=CCC/C(....
6 2E9C - B75 C24 H23 N O9 P2 S c1ccc2cc(c....
7 2E9A - B28 C20 H20 O7 P2 c1ccc(cc1)....
8 1X06 - FPS C15 H28 O6 P2 S CC(=CCC/C(....
9 1X07 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
10 2E98 - B29 C20 H18 O8 P2 c1ccc2c(c1....
11 3WYJ ic50 = 1.9 uM H78 C34 H36 N2 O18 P4 S2 c1cc(cc(c1....
12 1X08 Kd = 520 uM IPE C5 H12 O7 P2 CC(=C)CCO[....
13 2E99 - B08 C20 H20 O7 P2 c1ccc(cc1)....
14 4ONC Kd = 410 nM 40B C19 H18 O7 P2 c1ccc(cc1)....
15 2VG3 - GPP C10 H20 O7 P2 CC(=CCC/C(....
16 5HC8 - PIS H3 O6 P2 S OP(=O)(O)O....
17 5HC7 - DST C5 H14 O6 P2 S CC(C)CCS[P....
18 4Q9O Kd = 1.7 uM 2ZW C20 H19 Cl N2 O2 Cc1c(c(no1....
19 4Q9M Kd = 66 nM 2ZW C20 H19 Cl N2 O2 Cc1c(c(no1....
20 4U82 ic50 = 0.39 uM FPS C15 H28 O6 P2 S CC(=CCC/C(....
21 2VG1 - FPP C15 H28 O7 P2 CC(=CCC/C(....
22 2VG0 - GPP C10 H20 O7 P2 CC(=CCC/C(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: H78; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 H78 1 1
2 B75 0.722222 0.966102
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3WYJ; Ligand: H78; Similar sites found: 181
This union binding pocket(no: 1) in the query (biounit: 3wyj.bio1) has 64 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4OAS 2SW 0.009611 0.44661 None
2 4LWU 20U 0.01582 0.43527 None
3 4ELG 52J 0.007225 0.43283 None
4 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 0.02831 0.42891 None
5 1EYQ NAR 0.03824 0.42532 None
6 4ELG 52I 0.007337 0.41923 None
7 4HBM 0Y7 0.04273 0.40668 None
8 1GMN IDS SGN IDS SGN IDS 0.01736 0.44743 1.0929
9 2PRG BRL 0.004138 0.4578 1.18577
10 5KJW 53C 0.02921 0.43732 1.18577
11 5TWO 7MV 0.01116 0.42983 1.18577
12 3W68 VIV 0.01189 0.42274 1.18577
13 2HFP NSI 0.01382 0.41703 1.18577
14 2PR5 FMN 0.01041 0.43441 1.51515
15 1TMX HGX 0.00865 0.43212 1.58103
16 3KMZ EQO 0.01754 0.40513 1.58103
17 4DSU BZI 0.02166 0.44377 1.5873
18 3IA4 MTX 0.02461 0.42519 1.85185
19 4V3I ASP LEU THR ARG PRO 0.0219 0.4448 1.97628
20 3B12 FAH 0.03866 0.42904 1.97628
21 3HYW DCQ 0.04571 0.42451 1.97628
22 3G58 988 0.02499 0.41852 1.97628
23 3LLI FAD 0.02151 0.40124 1.97628
24 4WUJ FMN 0.003601 0.45711 2.04082
25 2OKL BB2 0.03789 0.40935 2.16216
26 1S17 GNR 0.02154 0.41881 2.22222
27 1Y7P RIP 0.02991 0.41421 2.24215
28 1TV5 N8E 0.001124 0.52509 2.37154
29 2G30 ALA ALA PHE 0.0002126 0.48462 2.37154
30 5K53 STE 0.00869 0.43508 2.37154
31 1QY8 RDI 0.02426 0.42227 2.37154
32 1NHZ 486 0.01654 0.42154 2.37154
33 4QVX 3CQ 0.02505 0.4101 2.39521
34 1U3R 338 0.02089 0.42246 2.48963
35 2YJD YJD 0.0217 0.42477 2.5
36 5M6N 7H9 0.01254 0.45778 2.54237
37 4DR9 BB2 0.01969 0.42693 2.60417
38 4MTI 2DX 0.01529 0.45376 2.6087
39 3IX9 MTX 0.02426 0.41917 2.63158
40 5VRH OLB 0.005606 0.4808 2.7668
41 2WKQ FMN 0.0051 0.44968 2.7668
42 3BMQ AX5 0.03243 0.43295 2.7668
43 3SP6 IL2 0.0141 0.42792 2.7668
44 5LOF 70R 0.004811 0.42459 2.7668
45 2WPW ACO 0.02673 0.42009 2.7668
46 2WPX ACO 0.03413 0.41166 2.7668
47 2BEK ATP 0.03615 0.40245 2.7668
48 4E2J MOF 0.02652 0.40892 2.8
49 3B6C SDN 0.004203 0.48419 2.99145
50 5ICK FEZ 0.03626 0.40755 3.05677
51 4XPL ACO 0.006602 0.44763 3.06748
52 4F0B GDS 0.0303 0.40615 3.125
53 1M2Z BOG 0.0006877 0.54349 3.16206
54 1GPM AMP 0.0008177 0.52638 3.16206
55 2J5V PCA 0.01645 0.47191 3.16206
56 4MGA 27L 0.01115 0.46604 3.16206
57 4TUZ 36J 0.01431 0.44125 3.16206
58 2OS2 OGA 0.03629 0.43256 3.16206
59 2YBP 2HG 0.03721 0.43169 3.16206
60 4MG8 27J 0.01859 0.4316 3.16206
61 5DXE EST 0.023 0.42674 3.16206
62 1KPG 16A 0.01747 0.42639 3.16206
63 5HYR EST 0.02886 0.42154 3.16206
64 4MGD 27N 0.03169 0.41939 3.16206
65 1UWC FER 0.03724 0.41891 3.16206
66 4MG7 27H 0.02992 0.41456 3.16206
67 4MGB XDH 0.04716 0.40449 3.16206
68 4XRZ SI6 0.03588 0.4002 3.16206
69 2BJ4 OHT 0.004179 0.45044 3.1746
70 4TV1 36M 0.007483 0.4699 3.18725
71 3UUD EST 0.03023 0.42047 3.18725
72 2HJ3 FAD 0.01533 0.42029 3.2
73 3GN8 DEX 0.03592 0.40511 3.21285
74 5UFS 1TA 0.03474 0.40086 3.22581
75 5LX9 OLA 0.00416 0.46154 3.55731
76 1BII ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 0.00234 0.44052 3.55731
77 3OQJ 3CX 0.03154 0.43405 3.55731
78 5LX9 OLB 0.02526 0.42459 3.55731
79 4D81 ADP 0.02195 0.42451 3.55731
80 4EIL FOL 0.02118 0.42216 3.55731
81 4EIL CB3 0.04408 0.41827 3.55731
82 4GBD MCF 0.02087 0.4139 3.55731
83 1MHC FME TYR PHE ILE ASN ILE LEU THR LEU 0.01355 0.40135 3.55731
84 1D1G MTX 0.03183 0.42259 3.57143
85 4O4Z N2O 0.01866 0.43836 3.8961
86 1ID0 ANP 0.04383 0.41507 3.94737
87 3TDC 0EU 0.00005997 0.59215 3.95257
88 2WSI FAD 0.03097 0.40569 3.95257
89 5UC9 MYR 0.01155 0.46192 3.9823
90 4WQ2 3SU 0.003669 0.46042 4.04624
91 2V0U FMN 0.005419 0.44838 4.10959
92 4UA3 COA 0.03042 0.40865 4.12371
93 1G27 BB1 0.01481 0.42685 4.16667
94 3SJK LYS PRO VAL LEU ARG THR ALA 0.006511 0.47614 4.21053
95 2CNT COA 0.0245 0.40094 4.375
96 2GBB CIT 0.02139 0.43956 4.48718
97 1M48 FRG 0.005943 0.47561 4.51128
98 4DOL PLM 0.026 0.41765 4.60829
99 2NZ5 226 0.01376 0.44012 4.74308
100 4GCZ FMN 0.01162 0.43207 4.74308
101 5B25 4QJ 0.03002 0.41748 4.74308
102 5IXK 6EW 0.004991 0.41918 4.82456
103 5UNJ RJW 0.04967 0.40611 4.89796
104 5MWE TCE 0.02221 0.44283 4.93827
105 3RET PYR 0.007756 0.45147 4.9505
106 3RET SAL 0.007756 0.45147 4.9505
107 1DQE BOM 0.0404 0.40261 5.10949
108 3P7N FMN 0.008065 0.43665 5.13834
109 1XMU ROF 0.03648 0.41616 5.13834
110 2YOO K2B 0.02988 0.41174 5.13834
111 3KXC PLM 0.007997 0.42521 5.15464
112 4Q86 AMP 0.009159 0.4477 5.5336
113 5F2T PLM 0.02442 0.4133 5.5336
114 4C2X NHW 0.003225 0.40973 5.5336
115 3DFR MTX 0.03927 0.41766 5.55556
116 5K52 OCD 0.01008 0.42896 5.66038
117 1RDT L79 0.03037 0.40868 5.78512
118 4NSQ COA 0.03764 0.40949 5.78947
119 4DOO DAO 0.03544 0.41682 5.85366
120 1PVC ILE SER GLU VAL 0.0101 0.468 5.88235
121 1J78 VDY 0.01337 0.45099 5.92885
122 3HR1 PF9 0.007617 0.43474 5.92885
123 3LJU IP9 0.039 0.43125 5.92885
124 3JRX S1A 0.01835 0.42531 5.92885
125 1DKF BMS 0.01689 0.4156 6.00858
126 4CVZ TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 0.001566 0.42999 6.12245
127 3B5J 12D 0.03141 0.43416 6.17284
128 3T50 FMN 0.03468 0.40852 6.25
129 1IYK MYA 0.0006994 0.45413 6.32411
130 3R9V DXC 0.04652 0.42332 6.32411
131 2C9E PID 0.03297 0.40193 6.32411
132 1LQY BB2 0.03216 0.41297 6.52174
133 5CHR 4NC 0.03144 0.43437 6.56934
134 4QC6 30N 0.01747 0.41491 6.70391
135 3WJO IPE 0.03919 0.42869 6.71937
136 4EJ1 FOL 0.02701 0.41985 6.91824
137 1KJM ALA GLN PHE SER ALA SER ALA SER ARG 0.006348 0.41716 7
138 5AWV GHP 3MY 3FG GHP GHP OMY 3FG NAG MAN 0.03869 0.44471 7.11462
139 3QKD HI0 0.0203 0.40692 7.18232
140 3UW5 MAA CHG PRO 0DQ 0.006545 0.47429 7.50988
141 3W54 RNB 0.03287 0.41249 7.50988
142 4YMU ARG 0.0409 0.42772 7.91667
143 5V4R MGT 0.005792 0.48223 8.02469
144 3ZLR X0B 0.001284 0.43101 8.22785
145 2GMH UQ5 0.01156 0.42331 8.3004
146 2A3I C0R 0.02954 0.40668 8.3004
147 3T4L ZEA 0.04561 0.40523 8.3004
148 5LWY OLB 0.02186 0.42789 8.41121
149 5LWY OLA 0.02545 0.41521 8.41121
150 5E5U MLI 0.02781 0.43159 8.54271
151 5UGW GSH 0.03134 0.43199 8.57143
152 2VWA PTY 0.02577 0.4365 8.91089
153 5FUI APY 0.02014 0.41597 9.09091
154 3B9O FMN 0.04514 0.40546 9.09091
155 5F7Y GLC GAL NAG GAL FUC A2G 0.03086 0.42332 9.16667
156 4I67 G G G RPC 0.003168 0.48087 9.1954
157 2CB8 MYA 0.02978 0.43914 9.1954
158 3RY9 1CA 0.04189 0.40712 9.2
159 4IBF 1D5 0.02416 0.42561 9.30233
160 5K04 COA 0.01349 0.42016 9.48617
161 1FQK ALF 0.02954 0.43558 9.52381
162 3ZJ0 ACO 0.01502 0.41285 9.70874
163 2PZE ATP 0.01566 0.45414 11.3537
164 5DKK FMN 0.003017 0.46088 11.7241
165 5CYV WCA 0.01438 0.41623 12.3288
166 5OCA 9QZ 0.001451 0.52362 12.9032
167 2B96 ANN 0.02141 0.41337 13.0081
168 1NRL SRL 0.003996 0.45488 13.0435
169 4V1T ADP 0.04193 0.4071 13.834
170 5C9J STE 0.01984 0.4177 14.1414
171 3BZF VAL MET ALA PRO ARG ALA LEU LEU LEU 0.001837 0.432 14.433
172 1J54 TMP 0.01628 0.43119 14.5161
173 1YC4 43P 0.009309 0.45123 14.6245
174 4XCL AGS 0.04396 0.4008 16.6008
175 4YSX E23 0.01453 0.45341 16.6667
176 5DJU FMN 0.02779 0.41057 18.0328
177 5EFW FMN 0.005304 0.44884 18.3333
178 3KO0 TFP 0.04618 0.42427 18.8119
179 1XVB 3BR 0.0256 0.43131 21.3439
180 2BVE PH5 0.02694 0.43385 23.5294
181 2Q8E OGA 0.03655 0.43226 31.25
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