Receptor
PDB id Resolution Class Description Source Keywords
1E1O 2.12 Å EC: 6.1.1.6 LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM, COMPLEXED WITH ESCHERICHIA COLI LIGASE AMINOACYL-TRNA SYNTHETASE PROTEIN BIOSYNTHESIS
Ref.: ACTIVE SITE OF LYSYL-TRNA SYNTHETASE: STRUCTURAL ST THE ADENYLATION REACTION BIOCHEMISTRY V. 39 8418 2000
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:520;
A:521;
A:522;
A:523;
A:524;
A:525;
A:526;
A:527;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
LYS A:510;
Valid;
none;
submit data
147.195 C6 H15 N2 O2 C(CC[...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1E1O 2.12 Å EC: 6.1.1.6 LYSYL-TRNA SYNTHETASE (LYSU) HEXAGONAL FORM, COMPLEXED WITH ESCHERICHIA COLI LIGASE AMINOACYL-TRNA SYNTHETASE PROTEIN BIOSYNTHESIS
Ref.: ACTIVE SITE OF LYSYL-TRNA SYNTHETASE: STRUCTURAL ST THE ADENYLATION REACTION BIOCHEMISTRY V. 39 8418 2000
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 1E1T - LAD C16 H26 N7 O8 P c1nc(c2c(n....
2 1E24 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
3 1E1O - LYS C6 H15 N2 O2 C(CC[NH3+]....
4 1E22 - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3E9H - KAA C16 H26 N8 O7 S c1nc(c2c(n....
2 3E9I - XAH C16 H27 N8 O8 P c1nc(c2c(n....
3 1E1T - LAD C16 H26 N7 O8 P c1nc(c2c(n....
4 1E24 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
5 1E1O - LYS C6 H15 N2 O2 C(CC[NH3+]....
6 1E22 - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3E9H - KAA C16 H26 N8 O7 S c1nc(c2c(n....
2 3E9I - XAH C16 H27 N8 O8 P c1nc(c2c(n....
3 3BJU - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 1E1T - LAD C16 H26 N7 O8 P c1nc(c2c(n....
5 1E24 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
6 1E1O - LYS C6 H15 N2 O2 C(CC[NH3+]....
7 1E22 - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: LYS; Similar ligands found: 44
No: Ligand ECFP6 Tc MDL keys Tc
1 LYS 1 1
2 LYN 0.612903 0.741935
3 DLY 0.59375 0.962963
4 API 0.586207 0.733333
5 DHH 0.575758 0.709677
6 NPI 0.558824 0.709677
7 ORN 0.53125 0.925926
8 M3L 0.527778 0.604651
9 NLE 0.515152 0.677419
10 6HN 0.513514 0.604651
11 MLY 0.513514 0.641026
12 MLZ 0.513514 0.764706
13 ALY 0.512821 0.742857
14 11C 0.5 0.677419
15 6CL 0.5 0.766667
16 UN1 0.5 0.677419
17 HRG 0.475 0.764706
18 ONH 0.472222 0.694444
19 EXY 0.463415 0.621622
20 NOT 0.463415 0.764706
21 26P 0.459459 0.617647
22 HSE 0.451613 0.6875
23 DAB 0.451613 0.827586
24 CIR 0.447368 0.694444
25 HCS 0.4375 0.758621
26 NVA 0.4375 0.666667
27 2NP 0.435897 0.611111
28 ARG 0.435897 0.764706
29 DAR 0.435897 0.764706
30 REZ 0.422222 0.621622
31 5CT 0.413043 0.742857
32 DGL 0.411765 0.645161
33 GGL 0.411765 0.645161
34 DGN 0.411765 0.636364
35 GLN 0.411765 0.636364
36 GLU 0.411765 0.645161
37 ILO 0.404762 0.714286
38 SHR 0.404255 0.8125
39 0TF 0.404255 0.722222
40 2RA 0.4 0.733333
41 ABA 0.4 0.62069
42 DSN 0.4 0.645161
43 SER 0.4 0.645161
44 DBB 0.4 0.62069
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1E1O; Ligand: LYS; Similar sites found: 207
This union binding pocket(no: 1) in the query (biounit: 1e1o.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1YBH FAD 0.001974 0.40487 0.992063
2 2DKH FAD 0.000935 0.40804 1.19048
3 2BH9 NAP 0.00321 0.40864 1.22699
4 4HA6 FAD 0.001709 0.41106 1.38889
5 2CJA ATP 0.0006359 0.40586 1.38889
6 1SB8 UD2 0.005389 0.40143 1.42045
7 1Q0H NDP 0.001978 0.41273 1.47783
8 4JK3 NAD 0.0003524 0.4154 1.5444
9 2CJ9 SSA 0.000002751 0.49494 1.5873
10 2RGH FAD 0.001709 0.40797 1.5873
11 1F8F NAD 0.005658 0.40225 1.61725
12 3PLN U5P 0.01195 0.40771 1.65094
13 1V9N NDP 0.001048 0.40515 1.66667
14 2F2U M77 0.004606 0.41559 1.74129
15 1KOL NAD 0.001124 0.40931 1.75879
16 3K37 BCZ 0.00714 0.41141 1.76322
17 2C31 TZD 0.0008743 0.44102 1.78571
18 2C31 ADP 0.003503 0.419 1.78571
19 3F3E LEU 0.002038 0.40221 1.78571
20 1Y42 TYR 0.01673 0.40142 1.78571
21 1LDM NAD 0.007764 0.40305 1.82371
22 3OND ADN 0.00236 0.41017 1.84426
23 3OND NAD 0.00236 0.41017 1.84426
24 1SES AHX 0.00001766 0.53766 1.90024
25 1SES AMP 0.001228 0.47252 1.90024
26 3TEG DAH 0.000001272 0.51346 1.92771
27 2I4O ATP 0.0000003632 0.47635 1.96507
28 2J3M ATP 0.0000006037 0.5354 1.98413
29 2J3M PRI 0.000001248 0.52939 1.98413
30 1O9U ADZ 0.01268 0.4356 2
31 4NTD FAD 0.0002116 0.43502 2.05882
32 2Q1W NAD 0.001352 0.40169 2.1021
33 4DQ2 BTX 0.000528 0.44177 2.13415
34 3EAU NDP 0.01425 0.40058 2.14067
35 3EAU PDN 0.01425 0.40058 2.14067
36 3IAL PR8 0.00004599 0.4665 2.18254
37 3WE0 FAD 0.002214 0.40736 2.18254
38 1ME8 RVP 0.00738 0.41089 2.18688
39 2E5A LAQ 0.001171 0.42639 2.30548
40 1RYD GLC 0.0113 0.43286 2.32558
41 3P7N FMN 0.005981 0.41327 2.32558
42 1XHL NDP 0.0003328 0.42071 2.3569
43 1P4C FMN 0.006115 0.40796 2.36842
44 3OV6 MK0 0.002142 0.41878 2.38095
45 3UH0 TSB 0.0000238 0.48048 2.3913
46 2C5S AMP 0.007164 0.4124 2.42131
47 2P2V CSF 0.001441 0.41912 2.43056
48 4CKU P2F 0.001845 0.41374 2.43161
49 1F5F DHT 0.000004046 0.43345 2.43902
50 2NVK FAD 0.0005605 0.42483 2.45902
51 3QO8 SSA 0.0000117 0.54593 2.47423
52 3HXU A5A 0.0000003228 0.58201 2.49433
53 1TDF FAD 0.001069 0.42072 2.53165
54 1TDF NAP 0.006638 0.40915 2.53165
55 3A1I UNU 0.0006005 0.4512 2.57937
56 3WBF API 0.0008585 0.40921 2.62295
57 1R6D DAU 0.001527 0.42 2.67062
58 1R6D NAD 0.005327 0.40238 2.67062
59 2G30 ALA ALA PHE 0.0000737 0.57844 2.71318
60 1V35 NAI 0.0008548 0.41885 2.73556
61 3O03 NAP 0.0006946 0.40319 2.74914
62 1C0I BE2 0.0004807 0.43127 2.75482
63 1C0I FAD 0.0004807 0.43127 2.75482
64 3Q9T FAY 0.001631 0.40645 2.77778
65 1G0N PHH 0.0005647 0.42473 2.82686
66 1G0N NDP 0.001101 0.41195 2.82686
67 3D3W NAP 0.001361 0.40292 2.86885
68 1PR9 NAP 0.001542 0.40121 2.86885
69 3FC4 EDO 0.0008484 0.42951 2.97619
70 1SNY NAP 0.0005218 0.40695 2.99625
71 1G8S MET 0.002176 0.45186 3.04348
72 4USQ FAD 0.001221 0.40569 3.04709
73 4BJZ P3A 0.01035 0.40229 3.06604
74 4BJZ FAD 0.01035 0.40229 3.06604
75 2X61 NGA GAL SIA 0.002182 0.41794 3.10078
76 1RYI FAD 0.0007847 0.42006 3.14136
77 1RYI GOA 0.003045 0.40279 3.14136
78 4J7H TLO 0.0001622 0.40696 3.18471
79 4COQ SAN 0.01001 0.42144 3.23887
80 1HDR NAD 0.001833 0.41473 3.27869
81 1H2B NAJ 0.0006448 0.41311 3.34262
82 1H82 FAD 0.001279 0.4259 3.38983
83 1H82 GZZ 0.001492 0.4259 3.38983
84 3DGB MUC 0.006191 0.40607 3.40314
85 4FR3 0V4 0.008081 0.40552 3.4188
86 1OFL NGK GCD 0.006369 0.43716 3.5343
87 3PVT 3HC 0.002376 0.40007 3.53698
88 2R0N TGC 0.03089 0.40214 3.5533
89 3I28 34N 0.001901 0.41239 3.57143
90 4G87 UD1 0.003147 0.40465 3.59281
91 1V6A TRE 0.003828 0.43455 3.61446
92 1EDO NAP 0.009974 0.40169 3.68852
93 4W6Z 8ID 0.001688 0.40247 3.7464
94 2YVF NAD 0.004783 0.40906 3.92157
95 2YVF FAD 0.004569 0.40906 3.92157
96 1REO FAD 0.002236 0.40312 4.11523
97 3QXC ATP 0.0002472 0.41502 4.13223
98 4F8L GAL 0.006527 0.46838 4.13793
99 1Z44 NPO 0.01936 0.44169 4.14201
100 2C7G ODP 0.0004608 0.4394 4.16667
101 2C7G FAD 0.001042 0.42815 4.16667
102 3KO8 NAD 0.001282 0.4024 4.16667
103 2XVE FAD 0.003632 0.41322 4.31034
104 4HWT 1B2 0.0008167 0.41042 4.35835
105 4AT0 FAD 0.0006901 0.42801 4.36508
106 4NAT 2W5 0.001787 0.40404 4.375
107 3A7R LAQ 0.001298 0.43418 4.45104
108 2J07 HDF 0.00371 0.40446 4.52381
109 2J07 FAD 0.00371 0.40446 4.52381
110 1UXG FUM 0.001757 0.40541 4.53074
111 1UXG NAD 0.001757 0.40541 4.53074
112 1WLE SRP 0.00001339 0.47209 4.59082
113 3MF2 AMP 0.000001215 0.52333 4.62428
114 4OYA 1VE 0.004966 0.4251 4.68085
115 2V6O FAD 0.0009859 0.43982 4.69799
116 2C1Q BTN 0.0008644 0.41648 4.7619
117 1EP2 ORO 0.001288 0.40496 4.82315
118 1I2L DCS 0.0001851 0.40152 4.83271
119 2VBQ BSJ 0.001647 0.40158 4.84848
120 2HMT NAI 0.003676 0.40373 4.86111
121 2R40 EPH 0.0002402 0.42288 4.94297
122 4PQG NAG 0.02408 0.40652 4.96032
123 2QV7 ADP 0.0035 0.40725 5.04451
124 4HIA FMN 0.006246 0.40491 5.11364
125 1B7Y FYA 0.00000009802 0.58426 5.15873
126 1PEA ACM 0.00498 0.44878 5.19481
127 1JYQ MAZ PTR PTM ASN 0.003366 0.40672 5.20833
128 1DLJ UGA 0.002758 0.40964 5.22388
129 1DLJ NAI 0.0041 0.40384 5.22388
130 2QHV OC9 0.006328 0.43624 5.2381
131 3KYG 5GP 5GP 0.01618 0.40037 5.28634
132 3R35 4CO 0.0002531 0.42294 5.29801
133 1VDC FAD 0.0004246 0.43506 5.40541
134 3F81 STT 0.0006362 0.50245 5.46448
135 3ZPG 5GP 0.04459 0.40721 5.49738
136 2GND MAN 0.02499 0.40927 5.55556
137 3IAE D7K 0.001099 0.40313 5.55556
138 1ZK7 FAD 0.0007102 0.42565 5.56745
139 1M5B BN1 0.001965 0.4195 5.70342
140 2HZQ STR 0.03676 0.40286 5.74713
141 1GAD NAD 0.0006727 0.40361 5.75758
142 3MPI GRA 0.004618 0.40449 5.79345
143 1JA9 NDP 0.001017 0.43669 5.83942
144 3WSJ MK1 0.003131 0.40606 6.03448
145 2JGS BTN 0.005334 0.42541 6.15385
146 2G86 UMP 0.003331 0.40603 6.32911
147 1T26 GBD 0.006544 0.41882 6.54762
148 1T26 NAI 0.006544 0.41882 6.54762
149 2Q37 3AL 0.005677 0.42697 6.62983
150 2E1A MSE 0.003482 0.42543 6.66667
151 4E28 0MZ 0.007679 0.42115 6.74603
152 4E28 9MZ 0.01228 0.41736 6.74603
153 3P3N AKG 0.004563 0.43712 6.87679
154 1KGQ SCO 0.01286 0.40114 6.93431
155 1LVL FAD 0.0009354 0.41967 6.9869
156 3SHR CMP 0.005264 0.41325 7.02341
157 3BY8 MLT 0.0008494 0.47826 7.04225
158 4PLG NAI 0.002229 0.40096 7.18563
159 4PLG OXM 0.002229 0.40096 7.18563
160 1UDB NAD 0.004802 0.40234 7.39645
161 1UDB UFG 0.004802 0.40234 7.39645
162 2IMP NAI 0.01204 0.40323 7.51566
163 3S9K CIT 0.001437 0.51603 7.62712
164 4Q0P 0MK 0.01162 0.40962 7.69231
165 2NCD ADP 0.004079 0.43333 7.85714
166 1K97 ASP 0.001074 0.44217 8.13187
167 1K97 CIR 0.001074 0.44217 8.13187
168 1FIQ MTE 0.0004784 0.41286 8.21918
169 1N9L FMN 0.006469 0.41175 8.25688
170 2Q97 ATP 0.0002575 0.40578 8.26667
171 1WPY BTN 0.0009365 0.42133 8.51064
172 1C1L GAL BGC 0.00102 0.47449 8.75912
173 2V5E SCR 0.02397 0.42838 8.91089
174 1SS4 CIT 0.001933 0.53847 9.15033
175 1SS4 GSH 0.002335 0.50354 9.15033
176 2EWM NAD 0.0009043 0.40576 9.23695
177 2RHQ GAX 0.0009565 0.43696 9.52381
178 1OAA OAA 0.001802 0.4103 9.65251
179 1RHC F42 ACN 0.0001226 0.43112 9.69697
180 4JH6 FCN 0.02789 0.40322 10.1449
181 3ZJX BOG 0.01786 0.42354 10.7266
182 2ZTG A5A 0.000005285 0.55519 10.9127
183 4IAW LIZ 0.01848 0.4084 11.7021
184 4H2V AMP 0.0000005198 0.53051 11.8182
185 3ZZS TRP 0.001507 0.40403 12.3077
186 4H2X G5A 0.0000008736 0.58347 12.6214
187 4H2W AMP 0.00000291 0.47309 12.6214
188 4H2W 5GP 0.00005225 0.44004 12.6214
189 3KPE TM3 0.02758 0.40112 12.8205
190 12AS AMP 0.0000003737 0.56365 13.3333
191 2Q1S NAI 0.001654 0.41153 13.5279
192 3LZW FAD 0.0007847 0.41668 14.4578
193 2QLX RM4 0.005904 0.43825 14.8148
194 2QQ0 ANP 0.001037 0.40391 16.3043
195 2QQ0 ADP 0.001178 0.40219 16.3043
196 2QQ0 TMP 0.001178 0.40219 16.3043
197 4F4S EFO 0.006571 0.41888 19.7368
198 2FYU FDN 0.003063 0.40162 24.359
199 4CS4 AXZ 0.000000009312 0.66074 24.4526
200 4CS4 ANP 0.000000005649 0.6589 24.4526
201 2BTO GTP 0.002146 0.40261 27.7778
202 1G51 AMO 0.00000001216 0.62272 30.1587
203 2XGT NSS 0.00000001512 0.60619 31.0345
204 3REU ATP 0.00000008275 0.5307 43.1973
205 1X54 4AD 0.00000009665 0.5786 44.0092
206 3NEM AMO 0.00000003098 0.60402 45.8904
207 3NEM ATP 0.000004684 0.45015 45.8904
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