Receptor
PDB id Resolution Class Description Source Keywords
3A5Y 1.9 Å EC: 6.1.1.6 CRYSTAL STRUCTURE OF GENX FROM ESCHERICHIA COLI IN COMPLEX W LYSYLADENYLATE ANALOG ESCHERICHIA COLI AMINOACYL-TRNA SYNTHETASE PARALOG TRANSLATION TRNA LYSYL-SYNTHETASE LYSYLADENYLATE ANALOG AMINOACYL-TRNA SYNTHETASLIGASE STRUCTURAL GENOMICS NPPSFA NATIONAL PROJECT ON PRSTRUCTURAL AND FUNCTIONAL ANALYSES RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI
Ref.: A PARALOG OF LYSYL-TRNA SYNTHETASE AMINOACYLATES A LYSINE RESIDUE IN TRANSLATION ELONGATION FACTOR P. NAT.STRUCT.MOL.BIOL. V. 17 1136 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
KAA A:1990;
B:1991;
C:1992;
D:1993;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd = 11 nM
474.492 C16 H26 N8 O7 S c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3A5Y 1.9 Å EC: 6.1.1.6 CRYSTAL STRUCTURE OF GENX FROM ESCHERICHIA COLI IN COMPLEX W LYSYLADENYLATE ANALOG ESCHERICHIA COLI AMINOACYL-TRNA SYNTHETASE PARALOG TRANSLATION TRNA LYSYL-SYNTHETASE LYSYLADENYLATE ANALOG AMINOACYL-TRNA SYNTHETASLIGASE STRUCTURAL GENOMICS NPPSFA NATIONAL PROJECT ON PRSTRUCTURAL AND FUNCTIONAL ANALYSES RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI
Ref.: A PARALOG OF LYSYL-TRNA SYNTHETASE AMINOACYLATES A LYSINE RESIDUE IN TRANSLATION ELONGATION FACTOR P. NAT.STRUCT.MOL.BIOL. V. 17 1136 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 3A5Y Kd = 11 nM KAA C16 H26 N8 O7 S c1nc(c2c(n....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3G1Z - AMP C10 H14 N5 O7 P c1nc(c2c(n....
2 3A5Y Kd = 11 nM KAA C16 H26 N8 O7 S c1nc(c2c(n....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3G1Z - AMP C10 H14 N5 O7 P c1nc(c2c(n....
2 3A5Y Kd = 11 nM KAA C16 H26 N8 O7 S c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: KAA; Similar ligands found: 215
No: Ligand ECFP6 Tc MDL keys Tc
1 KAA 1 1
2 SSA 0.804598 0.942529
3 GSU 0.802198 0.942529
4 5CA 0.786517 0.942529
5 DSZ 0.769231 0.920455
6 LSS 0.769231 0.9
7 A5A 0.752809 0.908046
8 VMS 0.736264 0.88764
9 54H 0.736264 0.88764
10 TSB 0.728261 0.897727
11 53H 0.728261 0.877778
12 52H 0.717391 0.877778
13 YSA 0.707071 0.920455
14 NVA LMS 0.705263 0.9
15 G5A 0.7 0.965116
16 NSS 0.694737 0.920455
17 LEU LMS 0.680412 0.879121
18 XAH 0.673267 0.853933
19 WSA 0.669811 0.931035
20 5AS 0.633333 0.898876
21 LAD 0.623762 0.852273
22 P5A 0.607843 0.988506
23 4YB 0.558559 0.921348
24 649 0.552632 0.94382
25 AHX 0.542857 0.8
26 SON 0.541667 0.786517
27 CA0 0.536082 0.755556
28 7MD 0.535714 0.833333
29 5AL 0.534653 0.764045
30 A 0.532609 0.75
31 AMP 0.532609 0.75
32 5X8 0.530612 0.704545
33 SRP 0.524272 0.806818
34 DSH 0.521277 0.75
35 AMP MG 0.521277 0.714286
36 ADX 0.520408 0.863636
37 SLU 0.520325 0.868132
38 SA8 0.52 0.695652
39 ABM 0.515789 0.733333
40 A2D 0.515789 0.752809
41 SAH 0.514852 0.727273
42 SRA 0.510638 0.775281
43 AN2 0.510204 0.764045
44 YLP 0.508621 0.815217
45 5N5 0.505747 0.689655
46 AOC 0.505263 0.674157
47 A12 0.505155 0.766667
48 AP2 0.505155 0.766667
49 BA3 0.505155 0.752809
50 AU1 0.50505 0.755556
51 AMO 0.504673 0.786517
52 NB8 0.5 0.78022
53 5CD 0.5 0.659091
54 AP5 0.5 0.752809
55 B4P 0.5 0.752809
56 XYA 0.5 0.689655
57 ADP 0.5 0.752809
58 ME8 0.5 0.774194
59 RAB 0.5 0.689655
60 ADN 0.5 0.689655
61 TXA 0.5 0.747253
62 SFG 0.5 0.712644
63 YLB 0.495798 0.815217
64 YLC 0.495798 0.833333
65 8QN 0.495327 0.764045
66 GAP 0.495146 0.775281
67 S4M 0.494845 0.712766
68 3DH 0.494624 0.655556
69 AYB 0.491803 0.806452
70 M33 0.49 0.744444
71 ADP MG 0.49 0.725275
72 DAL AMP 0.485981 0.744444
73 SAI 0.485437 0.7
74 ADP BEF 0.485149 0.709677
75 50T 0.485149 0.725275
76 ACP 0.485149 0.755556
77 BEF ADP 0.485149 0.709677
78 ATP 0.485149 0.752809
79 YLA 0.483607 0.815217
80 EP4 0.483516 0.641304
81 7MC 0.483333 0.815217
82 A4D 0.483146 0.689655
83 K15 0.481818 0.691489
84 3UK 0.481818 0.755556
85 S7M 0.481132 0.698925
86 SMM 0.481132 0.694737
87 SAM 0.480769 0.698925
88 ANP 0.480769 0.755556
89 PRX 0.480392 0.736264
90 AQP 0.480392 0.752809
91 AR6 0.480392 0.752809
92 APC 0.480392 0.766667
93 APR 0.480392 0.752809
94 5FA 0.480392 0.752809
95 A7D 0.48 0.735632
96 GJV 0.479592 0.714286
97 6RE 0.479167 0.703297
98 DTA 0.478261 0.704545
99 WAQ 0.477477 0.808989
100 4AD 0.477064 0.777778
101 PAJ 0.477064 0.734043
102 EEM 0.47619 0.663158
103 ADP PO3 0.475728 0.75
104 RBY 0.475728 0.766667
105 SAP 0.475728 0.777778
106 AGS 0.475728 0.777778
107 AD9 0.475728 0.736264
108 ADV 0.475728 0.766667
109 ARG AMP 0.474576 0.784946
110 YAP 0.473684 0.777778
111 FA5 0.473684 0.786517
112 DLL 0.472727 0.764045
113 62X 0.472727 0.677083
114 ATF 0.471698 0.728261
115 ATP MG 0.471154 0.725275
116 J7C 0.469388 0.711111
117 OOB 0.46789 0.764045
118 ANP MG 0.46729 0.73913
119 ACQ 0.466667 0.755556
120 TAT 0.466667 0.766667
121 A3S 0.465347 0.724138
122 9SN 0.464912 0.723404
123 0UM 0.463636 0.725275
124 TYM 0.46281 0.786517
125 M2T 0.462366 0.645161
126 FYA 0.460177 0.764045
127 PTJ 0.460177 0.723404
128 1ZZ 0.460177 0.755319
129 BIS 0.460177 0.75
130 00A 0.459459 0.731183
131 A22 0.458716 0.744444
132 MAP 0.458716 0.73913
133 ADP ALF 0.457944 0.702128
134 ALF ADP 0.457944 0.702128
135 MTA 0.457447 0.655556
136 VRT 0.457143 0.711111
137 KB1 0.45614 0.688172
138 MYR AMP 0.45614 0.736842
139 OAD 0.455357 0.755556
140 N0B 0.454545 0.815217
141 A3N 0.454545 0.666667
142 5SV 0.454545 0.741935
143 25A 0.454545 0.752809
144 YLY 0.453846 0.806452
145 KH3 0.453782 0.702128
146 VO4 ADP 0.453704 0.744444
147 ADP VO4 0.453704 0.744444
148 IOT 0.451613 0.806452
149 PR8 0.451327 0.842697
150 ADQ 0.45045 0.755556
151 A1R 0.45045 0.808989
152 AAT 0.448598 0.733333
153 3OD 0.447368 0.755556
154 SXZ 0.447368 0.698925
155 JB6 0.447368 0.788889
156 MHZ 0.446602 0.723404
157 48N 0.446281 0.741935
158 MAO 0.445545 0.741935
159 A3G 0.444444 0.735632
160 TYR AMP 0.444444 0.747253
161 ADP BMA 0.442478 0.736264
162 A3T 0.442308 0.693182
163 TAD 0.441667 0.771739
164 AMP DBH 0.440678 0.698925
165 TXE 0.439024 0.75
166 ALF ADP 3PG 0.439024 0.715789
167 LA8 ALF 3PG 0.439024 0.715789
168 ZAS 0.438776 0.688889
169 LAQ 0.438017 0.793478
170 7C5 0.436975 0.677419
171 LPA AMP 0.434426 0.774194
172 25L 0.431034 0.744444
173 6V0 0.430894 0.741935
174 NEC 0.43 0.651685
175 GEK 0.428571 0.741573
176 S8M 0.428571 0.741573
177 4UV 0.428571 0.73913
178 OMR 0.427419 0.747368
179 A A 0.426087 0.733333
180 AR6 AR6 0.421488 0.733333
181 4UU 0.421488 0.73913
182 D3Y 0.419643 0.707865
183 TXD 0.419355 0.75
184 DND 0.419355 0.747253
185 NAX 0.419355 0.763441
186 NXX 0.419355 0.747253
187 SO8 0.416667 0.67033
188 AF3 ADP 3PG 0.416 0.715789
189 COD 0.415385 0.808511
190 2VA 0.415094 0.677778
191 AHZ 0.414634 0.71875
192 3AM 0.414141 0.738636
193 T5A 0.414062 0.739583
194 3NZ 0.413793 0.703297
195 ATP A A A 0.411765 0.741573
196 5AD 0.411111 0.609195
197 AFH 0.409836 0.734043
198 7D5 0.408163 0.722222
199 UP5 0.408 0.73913
200 4UW 0.408 0.715789
201 NAI 0.408 0.731183
202 NAD IBO 0.407692 0.72043
203 A5D 0.407407 0.704545
204 7D7 0.406593 0.647727
205 GTA 0.406504 0.701031
206 4TA 0.40458 0.729167
207 A3P 0.403846 0.75
208 A2P 0.403846 0.738636
209 594 0.402985 0.864583
210 G3A 0.401639 0.723404
211 4TC 0.401575 0.741935
212 BT5 0.401515 0.787234
213 V3L 0.4 0.752809
214 67D 0.4 0.9
215 CNA 0.4 0.766667
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3A5Y; Ligand: KAA; Similar sites found: 117
This union binding pocket(no: 1) in the query (biounit: 3a5y.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2BOS GLA GAL GLC 0.002014 0.46212 None
2 2BOS GLA GAL 0.003 0.44773 None
3 4IEN GDP 0.0005895 0.46537 1.22699
4 3DWQ NGC GAL NGA POL AZI 0.007958 0.43788 1.5873
5 2YKL NLD 0.01201 0.41228 1.88679
6 5LUN OGA 0.01085 0.41849 2.02899
7 5HV7 RBL 0.005066 0.41241 2.02899
8 2PNC CLU 0.03878 0.40184 2.02899
9 4XMF HSM 0.003287 0.45357 2.17391
10 3G2Y GF4 0.02957 0.40254 2.28137
11 2ART LPA AMP 0.00007132 0.41272 2.29008
12 3HXU A5A 0.000000005653 0.65257 2.31884
13 4HWS 1B3 0.00001279 0.43922 2.31884
14 1JS8 MAN MAN BMA 0.02418 0.41967 2.31884
15 5T8U LPA 0.01362 0.40963 2.31884
16 1WLE SRP 0.0000003096 0.53581 2.6087
17 1RYD GLC 0.003946 0.45893 2.6087
18 3GD9 GLC BGC BGC BGC 0.007063 0.42346 2.89855
19 1VJ7 GPX 0.02218 0.41566 2.89855
20 5KJW 53C 0.02799 0.40697 2.89855
21 5TV6 PML 0.01556 0.41483 2.91667
22 2A9W UMP 0.01345 0.42428 3.0303
23 1RZX ACE VAL LYS GLU SER LEU VAL 0.01015 0.43235 3.06122
24 2E5A LAQ 0.001385 0.40537 3.18841
25 3OV6 MK0 0.006022 0.40337 3.18841
26 2WZ5 MET 0.0005109 0.51416 3.26797
27 1OFL NGK GCD 0.0119 0.41679 3.47826
28 2VDF OCT 0.00001313 0.60004 3.55731
29 1DDU DDU 0.02781 0.40191 3.77358
30 5J75 6GQ 0.01336 0.40279 3.78788
31 3CM2 X23 0.02598 0.4081 3.84615
32 5H2U 1N1 0.0108 0.40706 4.11985
33 1MFI FHC 0.03902 0.40083 4.38596
34 5F6U 5VK 0.002104 0.4799 4.4586
35 4NS0 PIO 0.01646 0.41446 4.51128
36 5C83 4YN 0.01375 0.41755 4.54545
37 1I1E DM2 0.005881 0.44131 4.63768
38 3T4L ZEA 0.002636 0.43133 4.81482
39 2ZTG A5A 0.000000008012 0.68011 4.92754
40 1B7Y FYA 0.000000001631 0.64669 4.92754
41 3CV2 COA 0.01483 0.42465 4.92754
42 1QKQ MAN 0.0006525 0.50704 4.92958
43 5JJU AMP 0.00316 0.44034 5
44 2VSL MAA LYS PRO PHE 0.02319 0.40596 5.20833
45 3TEG DAH 0.000008189 0.52662 5.21739
46 4MTI 2DX 0.02141 0.41256 5.21739
47 3OYW TDG 0.01411 0.42145 5.22388
48 5FUI APY 0.0016 0.44754 5.30303
49 4G0P U5P 0.01447 0.42113 5.44218
50 2CJA ATP 0.00003566 0.52151 5.50725
51 4OFJ HIS 0.022 0.40713 5.50725
52 4ZTD ALA GLY ALA GLY ALA 0.02964 0.40399 5.5336
53 2WGV CIT 0.009763 0.43249 5.64516
54 4MOB ADP 0.00002172 0.57285 5.7971
55 1YFS ALA 0.001693 0.45615 5.7971
56 4IAW LIZ 0.0095 0.42135 5.85106
57 2I4O ATP 0.0000000165 0.70603 6.08696
58 2CJ9 SSA 0.000001029 0.51877 6.08696
59 3A16 PXO 0.0006804 0.49268 6.08696
60 5HWV MBN 0.01561 0.41915 6.15385
61 3HCH RSM 0.03456 0.40276 6.16438
62 12AS AMP 0.0000000088 0.60744 6.36364
63 3QO8 SSA 0.0000001546 0.6304 6.37681
64 5H9Y BGC BGC BGC BGC 0.008345 0.41599 6.37681
65 5E89 TD2 0.008835 0.41111 6.37681
66 5DYO FLU 0.0311 0.40234 6.42202
67 5VAD PRO 0.001282 0.45441 6.66667
68 5VAD 91Y 0.0002234 0.42578 6.66667
69 2HZQ STR 0.03057 0.40564 6.89655
70 2J3M ATP 0.00000007092 0.60691 6.95652
71 2J3M PRI 0.000000186 0.58301 6.95652
72 2RHQ GAX 0.0002513 0.45939 7.14286
73 5JSP DQY 0.01399 0.42171 7.46269
74 1HXD BTN 0.008469 0.40842 7.47664
75 2QHV OC9 0.004528 0.4421 7.61905
76 1SES AHX 0.0000002001 0.62523 8.11594
77 1SES AMP 0.0000476 0.54235 8.11594
78 3ERR AMP 0.00003689 0.43783 8.11594
79 3UEC ALA ARG TPO LYS 0.01037 0.43688 8.21918
80 4RYV ZEA 0.003606 0.4422 8.3871
81 3UH0 TSB 0.000004932 0.5145 8.4058
82 5F7U GLC GLC 0.009249 0.43273 8.4058
83 5T96 79J 0.009551 0.43729 8.47953
84 4DSU BZI 0.002284 0.46953 8.69565
85 4RKX 3S9 0.02137 0.412 8.81226
86 5NCF 8T5 0.008092 0.43408 8.84956
87 2QHS OCA 0.00627 0.4303 8.86076
88 3MF2 AMP 0.0000008573 0.56193 9.56522
89 3IAL PR8 0.0000195 0.50553 9.56522
90 3SAO DBH 0.005837 0.44323 10
91 2G30 ALA ALA PHE 0.00006149 0.52459 10.0775
92 4YVN EBS 0.03767 0.4017 10.1449
93 4DS0 A2G GAL NAG FUC 0.01661 0.42918 10.4294
94 1ZNY GDP 0.01348 0.4225 10.628
95 3CBC DBS 0.01364 0.42383 12.1212
96 5E6O TRP GLU GLU LEU 0.01521 0.41533 12.7119
97 3REU ATP 0.000000004136 0.69306 12.9252
98 2BVE PH5 0.01096 0.41663 13.4454
99 4WOE ADP 0.01979 0.41582 14.4928
100 4K55 H6P 0.01049 0.42475 14.5161
101 3H0L ADP 0.005281 0.43871 14.8936
102 4RHS SIA SIA GAL 0.001493 0.48815 15.5738
103 3IWD M2T 0.03064 0.40328 16.1765
104 5H9P TD2 0.003182 0.45521 16.4557
105 4CS4 ANP 0.00000000001327 0.60365 17.1533
106 4CS4 AXZ 0.00000000002694 0.55081 17.1533
107 5M6M 7H8 0.0157 0.41462 17.3228
108 4H2V AMP 0.0000004571 0.57973 19.0909
109 5M6N 7H9 0.01506 0.42101 19.4915
110 1G51 AMO 0.0000000001631 0.70531 22.029
111 4H2X G5A 0.0000001621 0.6134 22.3301
112 4H2W AMP 0.00000231 0.57628 22.3301
113 4H2W 5GP 0.00006357 0.50429 22.3301
114 2XGT NSS 0.00000000007198 0.68613 28.4058
115 1X54 4AD 0.0000000006286 0.67564 34.4928
116 3NEM ATP 0.000000001802 0.75353 40.5797
117 3NEM AMO 0.00000000009322 0.69494 40.5797
Pocket No.: 2; Query (leader) PDB : 3A5Y; Ligand: KAA; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3a5y.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3A5Y; Ligand: KAA; Similar sites found: 12
This union binding pocket(no: 3) in the query (biounit: 3a5y.bio2) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3ZJX BOG 0.03288 0.40286 1.38408
2 4FFG 0U8 0.01687 0.42175 1.44928
3 4K91 SIN 0.0426 0.40403 2.60116
4 5FPE 3TR 0.002162 0.45877 2.89855
5 4OYA 1VE 0.01002 0.42279 4.05797
6 3EFS BTN 0.009556 0.40118 4.72103
7 1BC5 ACE ASN TRP GLU THR PHE 0.02816 0.40019 5.57621
8 4HWT 1B2 0.001904 0.40385 5.7971
9 5J3Z 6FQ 0.0261 0.40613 6.25
10 3QX9 ATP 0.003338 0.45601 7.24638
11 1OPB RET 0.008533 0.40014 8.20895
12 4ZH7 FUC GAL NAG GAL FUC 0.02253 0.40122 11.0145
Pocket No.: 4; Query (leader) PDB : 3A5Y; Ligand: KAA; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 3a5y.bio2) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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