Receptor
PDB id Resolution Class Description Source Keywords
5C5H 2.4 Å EC: 6.2.1.26 R195K E. COLI MENE WITH BOUND OSB-AMS ESCHERICHIA COLI (STRAIN K12) LIGASE
Ref.: MECHANISM OF MENE INHIBITION BY ACYL-ADENYLATE ANAL DISCOVERY OF NOVEL ANTIBACTERIAL AGENTS. BIOCHEMISTRY V. 54 6514 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:501;
B:502;
B:501;
Part of Protein;
Invalid;
Invalid;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
4YB A:502;
B:503;
Valid;
Valid;
none;
none;
ic50 = 0.025 uM
550.499 C21 H22 N6 O10 S c1ccc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5C5H 2.4 Å EC: 6.2.1.26 R195K E. COLI MENE WITH BOUND OSB-AMS ESCHERICHIA COLI (STRAIN K12) LIGASE
Ref.: MECHANISM OF MENE INHIBITION BY ACYL-ADENYLATE ANAL DISCOVERY OF NOVEL ANTIBACTERIAL AGENTS. BIOCHEMISTRY V. 54 6514 2015
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5C5H ic50 = 0.025 uM 4YB C21 H22 N6 O10 S c1ccc(c(c1....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5C5H ic50 = 0.025 uM 4YB C21 H22 N6 O10 S c1ccc(c(c1....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5C5H ic50 = 0.025 uM 4YB C21 H22 N6 O10 S c1ccc(c(c1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 4YB; Similar ligands found: 169
No: Ligand ECFP6 Tc MDL keys Tc
1 4YB 1 1
2 G5A 0.670103 0.931035
3 649 0.631579 0.932584
4 A5A 0.617647 0.918605
5 DSZ 0.603774 0.953488
6 SSA 0.596154 0.931035
7 54H 0.590476 0.897727
8 VMS 0.590476 0.897727
9 52H 0.590476 0.88764
10 GSU 0.587156 0.976471
11 53H 0.584906 0.88764
12 5CA 0.584906 0.931035
13 TSB 0.584906 0.908046
14 NVA LMS 0.583333 0.910112
15 5AS 0.575758 0.866667
16 LSS 0.574074 0.910112
17 NSS 0.574074 0.931035
18 LEU LMS 0.563636 0.888889
19 YSA 0.561404 0.953488
20 KAA 0.558559 0.921348
21 P5A 0.558559 0.911111
22 WSA 0.53719 0.964706
23 3UK 0.522124 0.825581
24 SLU 0.507692 0.898876
25 SON 0.495238 0.795455
26 AMP MG 0.490196 0.722222
27 AOC 0.490196 0.681818
28 AMP 0.485149 0.758621
29 A 0.485149 0.758621
30 SRA 0.480392 0.784091
31 CA0 0.476636 0.784091
32 DLL 0.474138 0.813953
33 ABM 0.471154 0.741573
34 A2D 0.471154 0.781609
35 OOB 0.469565 0.813953
36 GAP 0.468468 0.764045
37 S0N 0.466216 0.755102
38 AU1 0.462963 0.764045
39 ADX 0.462963 0.873563
40 M33 0.462963 0.752809
41 A12 0.462264 0.755556
42 BA3 0.462264 0.781609
43 AP2 0.462264 0.755556
44 TXA 0.462185 0.775281
45 50T 0.458716 0.733333
46 5X8 0.458716 0.732558
47 B4P 0.457944 0.781609
48 ADP 0.457944 0.761364
49 AP5 0.457944 0.781609
50 9SN 0.454545 0.788889
51 PRX 0.454545 0.744444
52 APC 0.454545 0.755556
53 WAQ 0.453782 0.797753
54 AN2 0.453704 0.772727
55 5CD 0.453608 0.666667
56 XYA 0.452632 0.678161
57 RAB 0.452632 0.678161
58 ADN 0.452632 0.678161
59 5AL 0.451327 0.793103
60 3DH 0.45098 0.662921
61 SAP 0.45045 0.786517
62 ADP PO3 0.45045 0.758621
63 AGS 0.45045 0.786517
64 1ZZ 0.45 0.744681
65 ADP MG 0.449541 0.733333
66 ADP ALF 0.447368 0.709677
67 ALF ADP 0.447368 0.709677
68 67D 0.44697 0.954023
69 ATP MG 0.446429 0.733333
70 ACP 0.445455 0.764045
71 ADP BEF 0.445455 0.717391
72 BEF ADP 0.445455 0.717391
73 ATP 0.445455 0.761364
74 AMP DBH 0.443548 0.764045
75 SRP 0.443478 0.816092
76 5N5 0.443299 0.659091
77 ANP 0.442478 0.764045
78 ACQ 0.442478 0.764045
79 5FA 0.441441 0.761364
80 AR6 0.441441 0.781609
81 AQP 0.441441 0.761364
82 APR 0.441441 0.781609
83 AMO 0.440678 0.816092
84 FA5 0.439024 0.837209
85 A4D 0.438776 0.678161
86 NB8 0.438017 0.808989
87 594 0.437956 0.835052
88 ADV 0.4375 0.775281
89 RBY 0.4375 0.775281
90 AD9 0.4375 0.744444
91 AHX 0.436975 0.788889
92 00A 0.436975 0.777778
93 7MD 0.436508 0.802198
94 A22 0.435897 0.772727
95 DAL AMP 0.435897 0.772727
96 DTA 0.435644 0.712644
97 MYR AMP 0.434426 0.726316
98 NXX 0.434109 0.795455
99 DND 0.434109 0.795455
100 8QN 0.432203 0.793103
101 25A 0.432203 0.781609
102 MTA 0.431373 0.662921
103 ANP MG 0.431034 0.747253
104 J7C 0.429907 0.681319
105 TAT 0.429825 0.775281
106 PR8 0.429752 0.791209
107 LAD 0.429752 0.8
108 ADQ 0.428571 0.784091
109 PAJ 0.428571 0.741935
110 4AD 0.428571 0.806818
111 YLB 0.427481 0.765957
112 YAP 0.427419 0.827586
113 FYA 0.42623 0.793103
114 ME8 0.42623 0.802198
115 EP4 0.425743 0.630435
116 A5D 0.424779 0.712644
117 SA8 0.424779 0.684783
118 6RE 0.424528 0.673913
119 TYR AMP 0.424 0.795455
120 MAP 0.423729 0.747253
121 NAX 0.423077 0.791209
122 ATF 0.422414 0.736264
123 M2T 0.421569 0.652174
124 OAD 0.421488 0.784091
125 SAH 0.421053 0.735632
126 5SV 0.420168 0.712766
127 SFG 0.419643 0.72093
128 VO4 ADP 0.418803 0.752809
129 ADP VO4 0.418803 0.752809
130 LAQ 0.418605 0.782609
131 0UM 0.416667 0.677419
132 A3N 0.416667 0.637363
133 YLP 0.415385 0.765957
134 3OD 0.414634 0.784091
135 PTJ 0.414634 0.75
136 BIS 0.414634 0.73913
137 EEM 0.413793 0.670213
138 590 0.413793 0.845361
139 GJV 0.412844 0.666667
140 XAH 0.412698 0.782609
141 25L 0.41129 0.772727
142 TAD 0.410853 0.76087
143 ADP BMA 0.409836 0.764045
144 K15 0.409836 0.663158
145 4UV 0.409449 0.786517
146 MAO 0.409091 0.712766
147 OMR 0.409091 0.736842
148 TYM 0.409091 0.837209
149 SAI 0.408696 0.707865
150 ARG AMP 0.407692 0.755319
151 NEC 0.407407 0.622222
152 A3G 0.407407 0.704545
153 DSH 0.407407 0.681319
154 S7M 0.40678 0.706522
155 SMM 0.40678 0.702128
156 A A 0.406504 0.761364
157 7C5 0.40625 0.741573
158 7MC 0.406015 0.784946
159 A1R 0.404959 0.758242
160 ATP A A A 0.404762 0.770115
161 48N 0.40458 0.769231
162 LPA AMP 0.40458 0.763441
163 BS5 0.404412 0.802083
164 SXZ 0.403226 0.706522
165 ZAS 0.401869 0.677778
166 6V0 0.401515 0.75
167 KB1 0.4 0.695652
168 S4M 0.4 0.649485
169 IOT 0.4 0.757895
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5C5H; Ligand: 4YB; Similar sites found: 116
This union binding pocket(no: 1) in the query (biounit: 5c5h.bio2) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5F7J ADE 0.02195 0.41546 1.25
2 2NU5 NAG 0.01344 0.40369 1.63934
3 3VSS FRU 0.03445 0.40437 2.20751
4 5FWJ MMK 0.03362 0.40035 2.20751
5 1UYY BGC BGC 0.0294 0.40741 2.29008
6 1YFS ALA 0.0279 0.41313 2.42826
7 2Y4N PAC 0.000181 0.47328 2.51716
8 2Y4N DLL 0.00003144 0.47132 2.51716
9 5MX4 HPA 0.01968 0.41986 2.57511
10 3ESS 18N 0.02696 0.41193 2.6087
11 1PT2 SUC 0.007024 0.42654 2.68456
12 5XVK 8GC 0.03061 0.4055 2.8169
13 4WYU SER TRP PHE GLN THR ASP LEU 0.01044 0.41065 2.83019
14 3PUN FUC GAL NDG FUC 0.03261 0.40734 2.8481
15 4B2G V1N 0.0004071 0.45418 2.86976
16 5H2U 1N1 0.01539 0.40276 2.99625
17 3E7S AT2 0.03554 0.40111 3.01624
18 5KOD AMP 0.0002265 0.4935 3.09051
19 5KOD IAC 0.02958 0.41798 3.09051
20 2IVD ACJ 0.02235 0.40561 3.09051
21 4OEV OXL 0.03844 0.40259 3.09051
22 3JQ3 ADP 0.01362 0.41642 3.27869
23 3LE7 ADE 0.0127 0.42437 3.44828
24 2G30 ALA ALA PHE 0.0004335 0.45665 3.48837
25 3KYG 5GP 5GP 0.01518 0.40304 3.52423
26 1I1E DM2 0.004686 0.4495 3.53201
27 4RT1 C2E 0.007351 0.41777 3.57143
28 5L83 ASP TRP GLU ILE VAL 0.0168 0.40801 3.57143
29 2Y4O DLL 0.00002113 0.50326 3.75276
30 3HQP FDP 0.02479 0.41135 3.75276
31 2QX0 APC 0.01986 0.40444 3.77358
32 2W5P CL8 0.03237 0.40154 4.02685
33 3T4L ZEA 0.001832 0.44168 4.07407
34 2V57 PRL 0.02467 0.41234 4.21053
35 3BJE URA 0.01544 0.42562 4.29799
36 1L5Y BEF 0.009143 0.41499 4.51613
37 2OBM ADP 0.0275 0.40445 4.61095
38 5LPG 71V 0.0235 0.4084 4.87805
39 5MJA 7O3 0.01362 0.40191 4.91803
40 2I6A 5I5 0.005973 0.40822 4.92754
41 1XXR MAN 0.006117 0.45254 4.96894
42 4EPM AMP 0.001077 0.43291 5.07726
43 5FUI APY 0.002221 0.4451 5.30303
44 1Y63 ADP 0.01764 0.41078 5.43478
45 2NLQ GLY 0.03147 0.40405 5.55556
46 1QKQ MAN 0.00884 0.41769 5.6338
47 2XG5 EC2 0.0395 0.40105 5.78035
48 2XG5 EC5 0.0395 0.40105 5.78035
49 4LOO SB4 0.008529 0.41121 5.81717
50 4DSU BZI 0.005139 0.4522 5.82011
51 5TQZ GLC 0.008374 0.43937 6
52 2Z6J TUI 0.006846 0.43138 6.0241
53 5LUB 3Y7 0.01937 0.41578 6.48855
54 1WUW TSU 0.01578 0.43117 6.66667
55 4ZU3 4SD 0.04189 0.40042 7.04846
56 4C2C ALA ALA ALA 0.01649 0.41529 7.17489
57 5KJW 53C 0.004251 0.45786 7.25995
58 3H0L ADP 0.008919 0.43006 7.44681
59 2QHV OC9 0.03103 0.40216 7.61905
60 2X5D PLP 0.03138 0.40763 7.72627
61 3G6N MET ALA SER 0.01352 0.42527 7.8534
62 5JCJ 6JM 0.03244 0.40513 8.38852
63 3CM2 X23 0.03907 0.40192 8.46154
64 5IFK HPA 0.03197 0.40661 8.65385
65 5TH5 MET 0.01057 0.43092 8.74525
66 1V9T SIN ALA PRO ALA NIT 0.03955 0.40054 9.03614
67 4ITH RCM 0.006729 0.406 9.18367
68 1MJT ITU 0.01111 0.41256 9.27152
69 5F6U 5VK 0.001412 0.48844 9.55414
70 3IWD M2T 0.03043 0.40661 10.2941
71 2OUA AES 0.03797 0.40841 10.6383
72 1PG4 PRX 0.000006307 0.41865 11.0375
73 1PG4 COA 0.000006307 0.41865 11.0375
74 5TVF CGQ 0.01916 0.41299 11.7647
75 3NZ1 3NY 0.00772 0.44465 13.7931
76 2PYY GLU 0.02416 0.40778 14.4737
77 5M6N 7H9 0.02591 0.41188 15.2542
78 5E5U MLI 0.0009172 0.42056 15.5779
79 5EY9 5SV 0.00000007344 0.59171 17.4393
80 5HM3 649 0.0000005136 0.52907 17.4393
81 4MTI 2DX 0.0256 0.41299 18.2609
82 4R0M FA5 0.00000002853 0.60166 22.0751
83 5D6J ATP 0.000006304 0.46543 22.973
84 5MST AMP 0.000001017 0.58281 26.4901
85 5MST FUM 0.000004379 0.52622 26.4901
86 3IES M24 0.000002327 0.54051 28.2561
87 4OXI GAP 0.00000387 0.49281 29.1391
88 5OE4 3UK 0.0000007192 0.57606 29.8013
89 3C5E ATP 0.0000004608 0.42298 30.2428
90 2D1S SLU 0.0000004114 0.53315 32.4503
91 4RLQ 3SK 0.0000006421 0.46616 32.4503
92 5MSD AMP 0.0000001546 0.63536 32.8918
93 5MSD BEZ 0.00000004733 0.63424 32.8918
94 4DG8 AMP 0.00004093 0.52268 33.5541
95 3DHV DAL AMP 0.0000005079 0.58253 35.9823
96 3KXW 1ZZ 0.000001522 0.53428 35.9823
97 3E7W AMP 0.000002856 0.58382 36.4238
98 5IE3 AMP 0.00000005218 0.59623 39.5143
99 5IE3 OXD 0.00000005218 0.59623 39.5143
100 3O84 HTJ 0.000006946 0.51325 39.7351
101 3NYQ MCA 0.0000003371 0.5193 40
102 3NYQ AMP 0.0000003561 0.51162 40
103 5N9X THR 0.000001451 0.63096 40.3974
104 5N9X 8QN 0.0000001495 0.59841 40.3974
105 5N9X ATP 0.0000004138 0.58634 40.3974
106 5BSR COA 0.0000004178 0.59968 41.7219
107 5BSR AMP 0.00000186 0.5555 41.7219
108 4GXQ ATP 0.0000005237 0.58196 42.3841
109 4FUT ATP 0.00000227 0.48968 42.6049
110 1V25 ANP 0.0000002751 0.50894 43.7086
111 4GR5 APC 0.00001723 0.5467 43.9294
112 1AMU AMP 0.0000003765 0.49644 44.5916
113 4D57 ARG AMP 0.00000004074 0.53236 45.4746
114 3CW9 AMP 0.000003825 0.56369 46.3576
115 3CW9 01A 0.00008547 0.4593 46.3576
116 1MDB AMP DBH 0.0000005152 0.58896 47.0199
Pocket No.: 2; Query (leader) PDB : 5C5H; Ligand: 4YB; Similar sites found: 27
This union binding pocket(no: 2) in the query (biounit: 5c5h.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4G8R 96P 0.006883 0.44577 2.12766
2 1NML CIT 0.02738 0.40771 2.14724
3 1W8S FBP 0.01401 0.40679 2.6616
4 3JU6 ANP 0.03418 0.40261 2.7027
5 2PHT MAN MAN MAN 0.01879 0.41827 2.77778
6 1GPM AMP 0.02056 0.40753 2.86976
7 4WOE ADP 0.03139 0.40599 2.86976
8 2R0D 4IP 0.01892 0.4119 2.88184
9 5TCI MLI 0.005146 0.45224 3.26087
10 2VDF OCT 0.004865 0.42484 3.55731
11 4YMZ 13P 0.02359 0.40698 3.58566
12 4JCA CIT 0.04351 0.40287 3.59281
13 4YG0 GAL NAG GAL BGC 0.03842 0.40657 3.65854
14 4ZTD ALA GLY ALA GLY ALA 0.04086 0.40332 3.95257
15 3P7G MAN 0.03814 0.40171 4.10959
16 4DS0 A2G GAL NAG FUC 0.02382 0.40339 4.29448
17 1FHX 4IP 0.0267 0.40038 4.65116
18 5EYW PGA 0.01648 0.41498 4.81928
19 4GLW NMN 0.02365 0.41434 4.91803
20 1OYF MHN 0.02622 0.40618 4.95868
21 3VSV XYS 0.0207 0.41605 5.07726
22 2BTM PGA 0.0265 0.40438 5.55556
23 1SBR VIB 0.02423 0.41053 7
24 1WQ1 AF3 0.0231 0.40945 7.18563
25 1LOP SIN ALA PRO ALA NIT 0.01446 0.42574 7.31707
26 2AIQ BEN 0.03227 0.40393 7.79221
27 4NAE 1GP 0.04013 0.40096 10.6667
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