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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: 229
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 LSS 0.769231 0.9
6 DSZ 0.769231 0.920455
7 A5A 0.752809 0.908046
8 VMS 0.736264 0.88764
9 54H 0.736264 0.88764
10 53H 0.728261 0.877778
11 TSB 0.728261 0.897727
12 52H 0.717391 0.877778
13 YSA 0.707071 0.920455
14 NVA LMS 0.705263 0.911111
15 G5A 0.7 0.965116
16 NSS 0.694737 0.920455
17 LEU LMS 0.680412 0.89011
18 XAH 0.673267 0.853933
19 WSA 0.669811 0.931035
20 8X1 0.639175 0.954545
21 5AS 0.633333 0.898876
22 8PZ 0.631068 0.920455
23 LAD 0.623762 0.852273
24 P5A 0.607843 0.988506
25 LMS 0.602273 0.906977
26 8Q2 0.575221 0.89011
27 4YB 0.558559 0.921348
28 649 0.552632 0.94382
29 AHX 0.542857 0.8
30 SON 0.541667 0.786517
31 CA0 0.536082 0.755556
32 7MD 0.535714 0.833333
33 5AL 0.534653 0.764045
34 AMP 0.532609 0.75
35 A 0.532609 0.75
36 5X8 0.530612 0.704545
37 SRP 0.524272 0.806818
38 DSH 0.521277 0.75
39 ADX 0.520408 0.863636
40 SLU 0.520325 0.868132
41 SA8 0.52 0.695652
42 A2D 0.515789 0.752809
43 ABM 0.515789 0.733333
44 SAH 0.514852 0.727273
45 SRA 0.510638 0.775281
46 AN2 0.510204 0.764045
47 YLP 0.508621 0.815217
48 5N5 0.505747 0.689655
49 AOC 0.505263 0.674157
50 AP2 0.505155 0.766667
51 A12 0.505155 0.766667
52 BA3 0.505155 0.752809
53 AU1 0.50505 0.755556
54 AMO 0.504673 0.786517
55 NB8 0.5 0.78022
56 SFG 0.5 0.712644
57 XYA 0.5 0.689655
58 AP5 0.5 0.752809
59 ADP 0.5 0.752809
60 ME8 0.5 0.774194
61 B4P 0.5 0.752809
62 TXA 0.5 0.747253
63 RAB 0.5 0.689655
64 5CD 0.5 0.659091
65 ADN 0.5 0.689655
66 YLC 0.495798 0.833333
67 YLB 0.495798 0.815217
68 8QN 0.495327 0.764045
69 9ZA 0.495327 0.75
70 9ZD 0.495327 0.75
71 GAP 0.495146 0.775281
72 AT4 0.494949 0.766667
73 S4M 0.494845 0.712766
74 3DH 0.494624 0.655556
75 AYB 0.491803 0.806452
76 M33 0.49 0.744444
77 DAL AMP 0.485981 0.744444
78 SAI 0.485437 0.7
79 ACP 0.485149 0.755556
80 50T 0.485149 0.725275
81 ATP 0.485149 0.752809
82 HEJ 0.485149 0.752809
83 YLA 0.483607 0.815217
84 EP4 0.483516 0.641304
85 7MC 0.483333 0.815217
86 A4D 0.483146 0.689655
87 K15 0.481818 0.691489
88 3UK 0.481818 0.755556
89 S7M 0.481132 0.698925
90 SMM 0.481132 0.694737
91 SAM 0.480769 0.698925
92 ANP 0.480769 0.755556
93 PRX 0.480392 0.736264
94 APC 0.480392 0.766667
95 APR 0.480392 0.752809
96 AR6 0.480392 0.752809
97 AQP 0.480392 0.752809
98 5FA 0.480392 0.752809
99 A7D 0.48 0.735632
100 GJV 0.479592 0.714286
101 6RE 0.479167 0.703297
102 DTA 0.478261 0.704545
103 WAQ 0.477477 0.808989
104 4AD 0.477064 0.777778
105 PAJ 0.477064 0.734043
106 EEM 0.47619 0.663158
107 F2R 0.475806 0.795699
108 AGS 0.475728 0.777778
109 SAP 0.475728 0.777778
110 ADV 0.475728 0.766667
111 RBY 0.475728 0.766667
112 AD9 0.475728 0.736264
113 ADP PO3 0.475728 0.75
114 YAP 0.473684 0.777778
115 FA5 0.473684 0.786517
116 9K8 0.473214 0.737374
117 DLL 0.472727 0.764045
118 62X 0.472727 0.677083
119 ATF 0.471698 0.728261
120 ARG AMP 0.470085 0.784946
121 J7C 0.469388 0.711111
122 OOB 0.46789 0.764045
123 TAT 0.466667 0.766667
124 T99 0.466667 0.766667
125 ACQ 0.466667 0.755556
126 A3S 0.465347 0.724138
127 9SN 0.464912 0.723404
128 0UM 0.463636 0.725275
129 TYM 0.46281 0.786517
130 M2T 0.462366 0.645161
131 1ZZ 0.460177 0.755319
132 FYA 0.460177 0.764045
133 PTJ 0.460177 0.723404
134 BIS 0.460177 0.75
135 00A 0.459459 0.731183
136 MAP 0.458716 0.73913
137 A22 0.458716 0.744444
138 ADP ALF 0.457944 0.702128
139 ALF ADP 0.457944 0.702128
140 MTA 0.457447 0.655556
141 VRT 0.457143 0.711111
142 KB1 0.45614 0.688172
143 MYR AMP 0.45614 0.736842
144 OAD 0.455357 0.755556
145 25A 0.454545 0.752809
146 A3N 0.454545 0.666667
147 5SV 0.454545 0.741935
148 N0B 0.454545 0.815217
149 YLY 0.453846 0.806452
150 KH3 0.453782 0.702128
151 VO4 ADP 0.453704 0.744444
152 ADP VO4 0.453704 0.744444
153 6YZ 0.453704 0.755556
154 IOT 0.451613 0.806452
155 B5V 0.451327 0.747253
156 PR8 0.451327 0.842697
157 A1R 0.45045 0.808989
158 ADQ 0.45045 0.755556
159 AAT 0.448598 0.733333
160 JB6 0.447368 0.788889
161 SXZ 0.447368 0.698925
162 3OD 0.447368 0.755556
163 MHZ 0.446602 0.723404
164 48N 0.446281 0.741935
165 MAO 0.445545 0.741935
166 A3G 0.444444 0.735632
167 9X8 0.442478 0.758242
168 ADP BMA 0.442478 0.736264
169 A3T 0.442308 0.693182
170 TAD 0.441667 0.771739
171 AMP DBH 0.440678 0.698925
172 TYR AMP 0.440678 0.758242
173 TXE 0.439024 0.75
174 ZAS 0.438776 0.688889
175 LAQ 0.438017 0.793478
176 A3R 0.4375 0.808989
177 7C5 0.436975 0.677419
178 B5Y 0.435897 0.73913
179 B5M 0.435897 0.73913
180 LPA AMP 0.434426 0.774194
181 25L 0.431034 0.744444
182 6V0 0.430894 0.741935
183 NEC 0.43 0.651685
184 S8M 0.428571 0.741573
185 GEK 0.428571 0.741573
186 4UV 0.428571 0.73913
187 OMR 0.427419 0.747368
188 A A 0.426087 0.733333
189 F0P 0.424 0.733333
190 EO7 0.421569 0.866667
191 4UU 0.421488 0.73913
192 GA7 0.421488 0.747253
193 AR6 AR6 0.421488 0.733333
194 D3Y 0.419643 0.707865
195 NXX 0.419355 0.747253
196 TXD 0.419355 0.75
197 DND 0.419355 0.747253
198 NAX 0.419355 0.763441
199 DQV 0.418033 0.764045
200 SO8 0.416667 0.67033
201 AF3 ADP 3PG 0.416 0.715789
202 COD 0.415385 0.808511
203 2VA 0.415094 0.677778
204 AHZ 0.414634 0.71875
205 3AM 0.414141 0.738636
206 T5A 0.414062 0.739583
207 3NZ 0.413793 0.703297
208 ATP A A A 0.411765 0.741573
209 5AD 0.411111 0.609195
210 AFH 0.409836 0.734043
211 80F 0.409091 0.739583
212 7D5 0.408163 0.722222
213 UP5 0.408 0.73913
214 NAI 0.408 0.731183
215 4UW 0.408 0.715789
216 NVA 2AD 0.407407 0.703297
217 A5D 0.407407 0.704545
218 7D7 0.406593 0.647727
219 GTA 0.406504 0.701031
220 4TA 0.40458 0.729167
221 A3P 0.403846 0.75
222 A2P 0.403846 0.738636
223 594 0.402985 0.864583
224 G3A 0.401639 0.723404
225 4TC 0.401575 0.741935
226 BT5 0.401515 0.787234
227 CNA 0.4 0.766667
228 V3L 0.4 0.752809
229 67D 0.4 0.9
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3A5Y; Ligand: KAA; Similar sites found with APoc: 187
This union binding pocket(no: 1) in the query (biounit: 3a5y.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 2BOS GLA GAL GLC None
2 6GNO XDI None
3 2BOS GLA GAL None
4 4IEN GDP 1.22699
5 3DWQ NGC GAL NGA POL AZI 1.5873
6 2YKL NLD 1.88679
7 5W75 SUC 2.02899
8 5LUN OGA 2.02899
9 5HV7 RBL 2.02899
10 5C9P FUC 2.02899
11 2OJW ADP 2.02899
12 2PNC CLU 2.02899
13 5LHT TIH 2.04082
14 4XMF HSM 2.17391
15 3G2Y GF4 2.28137
16 2ART LPA AMP 2.29008
17 1KNM LAT 2.30769
18 3HXU A5A 2.31884
19 2Z3U CRR 2.31884
20 4HWS 1B3 2.31884
21 1JS8 MAN MAN BMA 2.31884
22 1F9V ADP 2.31884
23 5T8U LPA 2.31884
24 5TCI MLI 2.53623
25 5EO8 TFU 2.57235
26 1WLE SRP 2.6087
27 1RYD GLC 2.6087
28 4RF7 ARG 2.6087
29 2JLD AG1 2.6087
30 1Y7P RIP 2.69058
31 6DZN AE3 2.8169
32 5G48 1FL 2.89855
33 3GD9 GLC BGC BGC BGC 2.89855
34 1VJ7 GPX 2.89855
35 5KJW 53C 2.89855
36 4MIB 28M 2.89855
37 5TV6 PML 2.91667
38 3PE2 E1B 2.96736
39 2A9W UMP 3.0303
40 1ZPR UMP 3.0303
41 1RZX ACE VAL LYS GLU SER LEU VAL 3.06122
42 6DW2 HD4 3.13725
43 2E5A LAQ 3.18841
44 5ZA2 NXL 3.18841
45 3OV6 MK0 3.18841
46 2GQS C2R 3.37553
47 1OFL NGK GCD 3.47826
48 5AHN IMP 3.47826
49 2VDF OCT 3.55731
50 4YDQ ANP 3.76812
51 4YDQ HFG 3.76812
52 5XIO HFG 3.76812
53 5XIJ ANP 3.76812
54 5XIJ 873 3.76812
55 5XIO ANP 3.76812
56 5YJS SAL 3.76812
57 1TDU DUR 3.77358
58 3KIF GDL 3.77358
59 1DDU DDU 3.77358
60 5J75 6GQ 3.78788
61 6EWZ APC 3.79747
62 3CM2 X23 3.84615
63 6E1Q CFA 4.05797
64 6GH9 MIX 4.05797
65 2J5B TYE 4.05797
66 3ZXR P3S 4.05797
67 3ZXR IQ1 4.05797
68 3L5R 47X 4.09836
69 5H2U 1N1 4.11985
70 1SDW IYT 4.14013
71 2AG4 LP3 4.26829
72 2AG4 OLA 4.26829
73 1J3I UMP 4.28571
74 5LXT GTP 4.34783
75 1MFI FHC 4.38596
76 5F6U 5VK 4.4586
77 3F5A SIA GAL NAG 4.47154
78 4NS0 PIO 4.51128
79 5C83 4YN 4.54545
80 1I1E DM2 4.63768
81 6BJO DUY 4.63768
82 2HJ4 PNZ 4.63768
83 3T4L ZEA 4.81482
84 1B7Y FYA 4.92754
85 2ZTG A5A 4.92754
86 3CV2 COA 4.92754
87 1QKQ MAN 4.92958
88 5JJU AMP 5
89 2VSL MAA LYS PRO PHE 5.20833
90 3TEG DAH 5.21739
91 4MTI 2DX 5.21739
92 3OYW TDG 5.22388
93 5FUI APY 5.30303
94 3UW4 MAA CHG PRO 0DQ 5.43478
95 4G0P U5P 5.44218
96 4P86 5GP 5.46448
97 2CJA ATP 5.50725
98 4OFJ HIS 5.50725
99 4ZTD ALA GLY ALA GLY ALA 5.5336
100 5ZHO A2G GLA FUC 5.55556
101 2WGV CIT 5.64516
102 1YFS ALA 5.7971
103 4HWT 1B2 5.7971
104 5LY1 PPI 5.7971
105 4MOB ADP 5.7971
106 4IAW LIZ 5.85106
107 3G08 FEE 5.96491
108 2I4O ATP 6.08696
109 2CJ9 SSA 6.08696
110 3A16 PXO 6.08696
111 1BW9 NAD 6.08696
112 4BTV RB3 6.10465
113 5HWV MBN 6.15385
114 3HCH RSM 6.16438
115 12AS AMP 6.36364
116 3QO8 SSA 6.37681
117 5H9Y BGC BGC BGC BGC 6.37681
118 5DYO FLU 6.42202
119 3A7R LAQ 6.52819
120 5VAD 91Y 6.66667
121 5VAD PRO 6.66667
122 2W9S TOP 6.8323
123 2HZQ STR 6.89655
124 2J3M ATP 6.95652
125 2J3M PRI 6.95652
126 4YRI 4JH 6.95652
127 2HIM ASP 6.95652
128 5JSP DQY 7.46269
129 1HXD BTN 7.47664
130 2QHV OC9 7.61905
131 5WL1 D3D 8.08081
132 5WL1 CUY 8.08081
133 4B2H C3F 8.10811
134 1SES AHX 8.11594
135 3ERR AMP 8.11594
136 1SES AMP 8.11594
137 3UEC ALA ARG TPO LYS 8.21918
138 4RYV ZEA 8.3871
139 3UH0 TSB 8.4058
140 5F7U GLC GLC 8.4058
141 1U6R ADP 8.4058
142 1WLJ U5P 8.46561
143 5T96 79J 8.47953
144 5OCG 9R5 8.69565
145 4RKX 3S9 8.81226
146 2QHS OCA 8.86076
147 1RJW ETF 9.14454
148 3MF2 AMP 9.56522
149 3IAL PR8 9.56522
150 4FE2 AIR 9.80392
151 3SAO DBH 10
152 2G30 ALA ALA PHE 10.0775
153 5V59 8X1 10.1449
154 4YVN EBS 10.1449
155 4DS0 A2G GAL NAG FUC 10.4294
156 1ZNY GDP 10.628
157 1LSH PLD 10.7246
158 3CBC DBS 12.1212
159 5E6O TRP GLU GLU LEU 12.7119
160 3REU ATP 12.9252
161 2BVE PH5 13.4454
162 5WHT SIA 13.7681
163 5WHT SIA GAL 13.7681
164 5WHT SIA GAL GLC 13.7681
165 3UW5 MAA CHG PRO 0DQ 13.7931
166 4WOE ADP 14.4928
167 4K55 H6P 14.5161
168 3H0L ADP 14.8936
169 5VM6 9EG 15.3285
170 4RHS SIA SIA GAL 15.5738
171 2HO2 PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU 15.7895
172 3IWD M2T 16.1765
173 5H9P TD2 16.4557
174 4CS4 ANP 17.1533
175 4CS4 AXZ 17.1533
176 6FA4 D1W 18.4971
177 4H2V AMP 19.0909
178 5EJL C2E 19.3548
179 5M6N 7H9 19.4915
180 1G51 AMO 22.029
181 4H2X G5A 22.3301
182 4H2W AMP 22.3301
183 4H2W 5GP 22.3301
184 2XGT NSS 28.4058
185 1X54 4AD 34.4928
186 3NEM AMO 40.5797
187 3NEM ATP 40.5797
Pocket No.: 2; Query (leader) PDB : 3A5Y; Ligand: KAA; Similar sites found with APoc: 20
This union binding pocket(no: 2) in the query (biounit: 3a5y.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 4GN8 ASO 1.67224
2 5FWJ MMK 1.73913
3 4NOS ITU 2.02899
4 2D24 XYS XYS 2.31884
5 3KYF 5GP 5GP 3.0303
6 2GJ5 VD3 3.08642
7 2ZL7 FUC GAL NGA 3.38983
8 3ACL 3F1 3.71622
9 4D4U FUC GAL NAG 4.12698
10 1RL4 BRR 4.25532
11 3O5N BR0 4.46429
12 3EFS BTN 4.72103
13 1BC5 ACE ASN TRP GLU THR PHE 5.57621
14 2VL1 GLY GLY 5.7971
15 3ZXE PGZ 6.01504
16 4XTX 590 6.2963
17 4R38 RBF 6.42857
18 4Y24 TD2 13.6364
19 1UPR 4IP 14.6341
20 5ODY 9SK 15.942
Pocket No.: 3; Query (leader) PDB : 3A5Y; Ligand: KAA; Similar sites found with APoc: 34
This union binding pocket(no: 3) in the query (biounit: 3a5y.bio2) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 4OIT MAN None
2 5AYT L6Y 1.25786
3 3ZJX BOG 1.38408
4 4FFG 0U8 1.44928
5 3CQO FUC 2.04778
6 4F8L AES 2.06897
7 4K91 SIN 2.60116
8 3RWP ABQ 2.89389
9 5FPE 3TR 2.89855
10 4UCF GLA 3.18841
11 3R96 AMP 3.7234
12 3R96 ACO 3.7234
13 3TCT 3MI 3.93701
14 5EYW PGA 4.01606
15 4OYA 1VE 4.05797
16 1USF NAP 4.49438
17 4MVK ACE VAL PHE PHE ALA GLU ASP NH2 4.78723
18 6MJ7 ARG 5.45455
19 6EGU 43Y 5.7971
20 3GD8 GOL 5.8296
21 5J3Z 6FQ 6.25
22 2P7Q GG6 6.76692
23 2HIM ASN 6.95652
24 5EW9 5VC 7.01107
25 3QX9 ATP 7.24638
26 1VRP ADP 8.11594
27 1OPB RET 8.20895
28 2HRL SIA GAL SIA BGC NGA CEQ 9.44882
29 2BS5 BGC GAL FUC 10
30 5WHU SIA GAL 10.0671
31 2BTM PGA 10.7143
32 4ZH7 FUC GAL NAG GAL FUC 11.0145
33 5OQW A4E 17.3228
34 1PVC ILE SER GLU VAL 27.9412
Pocket No.: 4; Query (leader) PDB : 3A5Y; Ligand: KAA; Similar sites found with APoc: 12
This union binding pocket(no: 4) in the query (biounit: 3a5y.bio2) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 2BOS GLA GAL GLC NBU None
2 2C78 PUL 1.44928
3 6GW4 CHO 2.28013
4 1MJT ITU 2.31884
5 2JDU MFU 2.6087
6 2GU8 796 2.67062
7 3VV1 GAL FUC 3.125
8 4O12 2QG 3.47826
9 2YMZ LAT 4.61538
10 5IXG OTP 5.21739
11 5NC1 NAG 9.2827
12 3K56 IS3 10.9023
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