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Receptor
PDB id Resolution Class Description Source Keywords
4H2X 2.15 Å EC: 6.2.1.- CRYSTAL STRUCTURE OF ENGINEERED BRADYRHIZOBIUM JAPONICUM GLYCINE:[CARRIER PROTEIN] LIGASE COMPLEXED WITH CARRIER PROA GROBACTERIUM TUMEFACIENS AND AN ANALOGUE OF GLYCYL ADENYLA BRADYRHIZOBIUM JAPONICUM, AGROBACTERIU(STRAIN C58 / ATCC 33970) LIGASE ATP BINDING GLYCINE BINDING CARRIER PROTEIN AMINOSYNTHETASE SERYL-TRNA SYNTHETASE
Ref.: ADAPTATION OF AMINOACYL-TRNA SYNTHETASE CATALYTIC C CARRIER PROTEIN AMINOACYLATION. STRUCTURE V. 21 614 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:402;
B:403;
Invalid;
Invalid;
none;
none;
submit data
35.453 Cl [Cl-]
ZN B:401;
Part of Protein;
none;
submit data
65.409 Zn [Zn+2...
G5A B:402;
A:401;
Valid;
Valid;
none;
none;
submit data
403.371 C12 H17 N7 O7 S c1nc(...
PNS C:101;
D:101;
Invalid;
Invalid;
none;
none;
submit data
358.348 C11 H23 N2 O7 P S CC(C)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4H2X 2.15 Å EC: 6.2.1.- CRYSTAL STRUCTURE OF ENGINEERED BRADYRHIZOBIUM JAPONICUM GLYCINE:[CARRIER PROTEIN] LIGASE COMPLEXED WITH CARRIER PROA GROBACTERIUM TUMEFACIENS AND AN ANALOGUE OF GLYCYL ADENYLA BRADYRHIZOBIUM JAPONICUM, AGROBACTERIU(STRAIN C58 / ATCC 33970) LIGASE ATP BINDING GLYCINE BINDING CARRIER PROTEIN AMINOSYNTHETASE SERYL-TRNA SYNTHETASE
Ref.: ADAPTATION OF AMINOACYL-TRNA SYNTHETASE CATALYTIC C CARRIER PROTEIN AMINOACYLATION. STRUCTURE V. 21 614 2013
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 4H2X - G5A C12 H17 N7 O7 S c1nc(c2c(n....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 4H2X - G5A C12 H17 N7 O7 S c1nc(c2c(n....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 4H2X - G5A C12 H17 N7 O7 S c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: G5A; Similar ligands found: 263
No: Ligand ECFP6 Tc MDL keys Tc
1 G5A 1 1
2 A5A 0.746988 0.940476
3 SSA 0.738095 0.97619
4 54H 0.729412 0.918605
5 VMS 0.729412 0.918605
6 52H 0.729412 0.908046
7 LEU LMS 0.727273 0.920455
8 NSS 0.724138 0.952941
9 DSZ 0.724138 0.952941
10 5AS 0.721519 0.930233
11 53H 0.72093 0.908046
12 TSB 0.72093 0.929412
13 5CA 0.72093 0.97619
14 8X1 0.72093 0.965116
15 NVA LMS 0.715909 0.920455
16 8PZ 0.706522 0.952941
17 LSS 0.704545 0.931035
18 KAA 0.7 0.965116
19 LMS 0.688312 0.939759
20 GSU 0.681319 0.952941
21 P5A 0.681319 0.954023
22 4YB 0.670103 0.931035
23 YSA 0.645833 0.952941
24 649 0.643564 0.910112
25 8Q2 0.637255 0.920455
26 A 0.604938 0.776471
27 AMP 0.604938 0.776471
28 SRA 0.597561 0.802326
29 WSA 0.596154 0.964286
30 SON 0.593023 0.793103
31 CA0 0.586207 0.781609
32 ABM 0.583333 0.758621
33 A2D 0.583333 0.77907
34 5N5 0.578947 0.714286
35 RAB 0.573333 0.714286
36 ADN 0.573333 0.714286
37 XYA 0.573333 0.714286
38 AOC 0.571429 0.697674
39 5CD 0.571429 0.682353
40 GAP 0.571429 0.802326
41 A12 0.569767 0.772727
42 AP2 0.569767 0.772727
43 BA3 0.569767 0.77907
44 AU1 0.568182 0.781609
45 ADX 0.568182 0.894118
46 AP5 0.563218 0.77907
47 ADP 0.563218 0.77907
48 B4P 0.563218 0.77907
49 50T 0.561798 0.75
50 3DH 0.560976 0.678161
51 AN2 0.556818 0.790698
52 AT4 0.556818 0.793103
53 APR 0.555556 0.77907
54 AR6 0.555556 0.77907
55 A3G 0.552941 0.761905
56 A4D 0.551282 0.714286
57 M33 0.550562 0.770115
58 RBY 0.549451 0.772727
59 SAP 0.549451 0.804598
60 ADV 0.549451 0.772727
61 AGS 0.549451 0.804598
62 5AL 0.548387 0.790698
63 5X8 0.544444 0.729412
64 ACP 0.544444 0.781609
65 ATP 0.544444 0.77907
66 HEJ 0.544444 0.77907
67 SLU 0.54386 0.897727
68 DTA 0.54321 0.709302
69 DAL AMP 0.541667 0.770115
70 AHX 0.540816 0.827586
71 TXA 0.54 0.772727
72 PRX 0.538462 0.741573
73 AQP 0.538462 0.77907
74 5FA 0.538462 0.77907
75 APC 0.538462 0.772727
76 ANP 0.537634 0.781609
77 SRP 0.536842 0.835294
78 9ZA 0.536082 0.775281
79 9ZD 0.536082 0.775281
80 AD9 0.532609 0.761364
81 ADP PO3 0.532609 0.776471
82 EP4 0.530864 0.662921
83 4AD 0.530612 0.804598
84 AMO 0.530612 0.813953
85 DLL 0.525253 0.790698
86 NB8 0.524752 0.806818
87 M2T 0.52439 0.666667
88 6RE 0.523256 0.707865
89 ACQ 0.521277 0.781609
90 TAT 0.521277 0.793103
91 T99 0.521277 0.793103
92 VO4 ADP 0.520833 0.770115
93 ADP VO4 0.520833 0.770115
94 8QN 0.520408 0.790698
95 OOB 0.520408 0.790698
96 3UK 0.52 0.781609
97 MTA 0.518072 0.678161
98 DSH 0.517241 0.715909
99 ADQ 0.515152 0.781609
100 PAJ 0.515152 0.758242
101 LAD 0.514852 0.818182
102 J7C 0.511364 0.715909
103 A3N 0.511364 0.689655
104 ADP ALF 0.510417 0.725275
105 ATF 0.510417 0.752809
106 ALF ADP 0.510417 0.725275
107 MAP 0.510204 0.764045
108 A22 0.510204 0.770115
109 00A 0.51 0.755556
110 3OD 0.509804 0.781609
111 9K8 0.509804 0.760417
112 GJV 0.505618 0.7
113 S4M 0.505618 0.680851
114 6YZ 0.505155 0.781609
115 5SV 0.50505 0.709677
116 25A 0.50505 0.77907
117 OAD 0.504951 0.781609
118 XAH 0.504762 0.820225
119 7MD 0.504673 0.820225
120 SA8 0.5 0.681319
121 WAQ 0.5 0.775281
122 B5V 0.5 0.772727
123 9SN 0.5 0.747253
124 PR8 0.5 0.808989
125 PTJ 0.495146 0.747253
126 1ZZ 0.495146 0.723404
127 ME8 0.495146 0.78022
128 SAH 0.494737 0.712644
129 SFG 0.494624 0.697674
130 ZAS 0.494253 0.712644
131 ARG AMP 0.490741 0.771739
132 MYR AMP 0.490385 0.705263
133 9X8 0.490196 0.784091
134 ADP BMA 0.490196 0.761364
135 TYR AMP 0.485981 0.784091
136 A1R 0.485149 0.816092
137 A3R 0.485149 0.816092
138 EEM 0.484536 0.648936
139 MAO 0.483516 0.728261
140 NEC 0.483146 0.674419
141 7C5 0.481481 0.7
142 YAP 0.481132 0.804598
143 FA5 0.481132 0.813953
144 B5M 0.481132 0.764045
145 B5Y 0.481132 0.764045
146 SXZ 0.480769 0.684783
147 BIS 0.480769 0.736264
148 SAI 0.479167 0.685393
149 YLP 0.477477 0.782609
150 25L 0.47619 0.770115
151 594 0.475 0.833333
152 S7M 0.474747 0.684783
153 SMM 0.474747 0.680851
154 SAM 0.474227 0.684783
155 6V0 0.473214 0.766667
156 A7D 0.473118 0.72093
157 TAD 0.472727 0.777778
158 EO7 0.472527 0.896552
159 AMP DBH 0.472222 0.722222
160 4UV 0.472222 0.764045
161 A A 0.471154 0.758621
162 LAQ 0.468468 0.76087
163 5AD 0.468354 0.630952
164 MHZ 0.468085 0.691489
165 JB6 0.466667 0.795455
166 FYA 0.466667 0.790698
167 3AM 0.465909 0.764706
168 YLB 0.464912 0.782609
169 7MC 0.464912 0.802198
170 48N 0.464286 0.766667
171 LPA AMP 0.464286 0.741935
172 4UU 0.463636 0.764045
173 AR6 AR6 0.463636 0.758621
174 GEK 0.460784 0.727273
175 NXX 0.460177 0.772727
176 NAX 0.460177 0.769231
177 DND 0.460177 0.772727
178 DQV 0.459459 0.790698
179 A3S 0.457447 0.75
180 0UM 0.456311 0.692308
181 OMR 0.45614 0.715789
182 AF3 ADP 3PG 0.45614 0.73913
183 TXE 0.45614 0.775281
184 AHZ 0.455357 0.723404
185 AAT 0.454545 0.7
186 ATP A A A 0.453704 0.767442
187 A5D 0.453608 0.709302
188 YLC 0.452174 0.8
189 A2P 0.451613 0.764706
190 A3P 0.451613 0.776471
191 AFH 0.45045 0.758242
192 67D 0.449153 0.909091
193 A3T 0.447917 0.717647
194 K15 0.447619 0.659574
195 NAI 0.447368 0.755556
196 TXD 0.447368 0.775281
197 4UW 0.447368 0.73913
198 Y3J 0.445783 0.616279
199 F2R 0.445378 0.782609
200 7D7 0.444444 0.651163
201 IOT 0.444444 0.774194
202 V3L 0.444444 0.77907
203 TYM 0.443478 0.813953
204 7D5 0.443182 0.727273
205 COD 0.441667 0.776596
206 G3A 0.441441 0.747253
207 YLA 0.440678 0.782609
208 2AM 0.438202 0.755814
209 62X 0.438095 0.645833
210 GA7 0.4375 0.772727
211 G5P 0.4375 0.747253
212 AYB 0.436975 0.774194
213 CNA 0.436975 0.793103
214 UP5 0.434783 0.764045
215 590 0.434109 0.84375
216 GTA 0.433628 0.723404
217 NAJ PZO 0.430894 0.747253
218 AMP NAD 0.429752 0.770115
219 NAD 0.429752 0.790698
220 4TC 0.42735 0.766667
221 UPA 0.42735 0.775281
222 A2R 0.427184 0.770115
223 BT5 0.42623 0.755319
224 DZD 0.42623 0.777778
225 PPS 0.425743 0.872093
226 BS5 0.425 0.83871
227 PAP 0.424242 0.767442
228 ATR 0.424242 0.755814
229 NVA 2AD 0.424242 0.707865
230 YLY 0.424 0.774194
231 OVE 0.423913 0.770115
232 A4P 0.423729 0.747368
233 3AD 0.423529 0.722892
234 A3D 0.422764 0.781609
235 KB1 0.422018 0.673913
236 A6D 0.420561 0.677419
237 S8M 0.419048 0.727273
238 2VA 0.418367 0.701149
239 BTX 0.418033 0.763441
240 NAJ PYZ 0.417323 0.715789
241 3NZ 0.416667 0.727273
242 139 0.416667 0.769231
243 T5A 0.416667 0.744681
244 AP0 0.415254 0.728261
245 2A5 0.414141 0.761364
246 N0B 0.414062 0.782609
247 M24 0.412698 0.75
248 80F 0.41129 0.763441
249 7D3 0.410526 0.730337
250 CC5 0.409639 0.710843
251 D3Y 0.409524 0.732558
252 NAE 0.409449 0.764045
253 KH3 0.408696 0.670213
254 7D4 0.408163 0.730337
255 4TA 0.406504 0.734043
256 NAQ 0.40625 0.747253
257 SO8 0.405941 0.693182
258 VRT 0.405941 0.715909
259 ADJ 0.404959 0.734043
260 J1D 0.403226 0.728155
261 ZID 0.403101 0.781609
262 IMO 0.4 0.744186
263 FB0 0.4 0.734694
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4H2X; Ligand: G5A; Similar sites found with APoc: 185
This union binding pocket(no: 1) in the query (biounit: 4h2x.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 5EZU MYR None
2 5GLT BGC GAL NAG GAL 1.40845
3 3WUC GLC GAL 2.18978
4 4K55 H6P 2.41935
5 3OJI PYV 2.6455
6 3ZJX BOG 2.76817
7 4O9S 2RY 2.7907
8 2D6M LBT 3.14465
9 2VO4 4NM 3.19635
10 2XGT NSS 3.67816
11 3REU ATP 3.7415
12 1MDC PLM 3.78788
13 5HWV MBN 3.84615
14 3NEM ATP 3.8835
15 3NEM AMO 3.8835
16 5TPV TYD 3.8835
17 3TEG DAH 3.8835
18 5UR6 8KM 3.8835
19 1A5Z FBP 3.8835
20 4WVO 3UZ 3.8835
21 4RDL FUC GAL NDG FUC 3.8835
22 3CH6 NAP 3.8835
23 3CH6 311 3.8835
24 3D91 REM 4.04624
25 2ZHL NAG GAL GAL NAG 4.05405
26 3L5R 47X 4.09836
27 1QKQ MAN 4.22535
28 3M3E GAL A2G NPO 4.34783
29 3OYW TDG 4.47761
30 6FOF LAT 4.59184
31 2YMZ LAT 4.61538
32 1ULE GLA GAL NAG 4.66667
33 3SAO DBH 4.85437
34 4L4J NAG NAG BMA MAN NAG 4.85437
35 1ELI PYC 4.85437
36 3WWC BUA 4.85437
37 3JQ3 ADP 4.85437
38 3SAO NKN 4.85437
39 3ZXR P3S 4.85437
40 3ZXR IQ1 4.85437
41 4AZP A9M 4.85437
42 6E08 NAP 4.85437
43 4HWT 1B2 4.91329
44 4YRI 4JH 4.91329
45 4ZTD ALA GLY ALA GLY ALA 5.20231
46 6MPT C30 5.59441
47 2ART LPA AMP 5.72519
48 6A63 LAT 5.7971
49 4JH6 FCN 5.7971
50 3HXU A5A 5.82524
51 5NFB 8VT 5.82524
52 5DG2 GAL GLC 5.82524
53 3LVW GSH 5.82524
54 5XDT MB3 5.82524
55 4W6Z ETF 5.82524
56 3QSB 743 5.82524
57 5DEY 59T 5.82524
58 4YLZ LAT NAG GAL 5.88235
59 1M6P M6P 5.92105
60 1U18 HSM 5.94595
61 1A78 TDG 5.97015
62 2AG4 OLA 6.09756
63 2AG4 LP3 6.09756
64 1QY1 PRZ 6.32184
65 5VAD 91Y 6.35838
66 5KEW 6SB 6.38298
67 3NV3 GAL NAG MAN 6.52174
68 1C1L GAL BGC 6.56934
69 2ZTG A5A 6.79612
70 2OVW CBI 6.79612
71 1OJJ GLC GAL 6.79612
72 1OJK GLC BGC 6.79612
73 5KJW 53C 6.79612
74 1R5L VIV 6.79612
75 5DMZ ADP 6.79612
76 2DXU BT5 6.80851
77 1J3R 6PG 6.84211
78 5N0L ILE 6.91824
79 4RYV ZEA 7.09677
80 6CAY ERG 7.10059
81 6GR0 F8W 7.47126
82 1B7Y FYA 7.76699
83 3WV6 GAL BGC 7.76699
84 3T4L ZEA 7.76699
85 6D61 4AA 7.76699
86 3WV6 GAL GLC 7.76699
87 3KFF XBT 7.76699
88 3KFF ZBT 7.76699
89 4RD0 GDP 7.76699
90 1SES AHX 7.83848
91 1SES AMP 7.83848
92 6FA4 D1W 8.09249
93 6GNO XDI 8.14815
94 1GT4 UNA 8.1761
95 6D6L FY4 8.23529
96 3BJU ATP 8.3815
97 1Y2F WAI 8.63309
98 1G51 AMO 8.73786
99 5DBX ANP 8.73786
100 1P0Z FLC 8.73786
101 1IS3 LAT 8.88889
102 3G08 FEE 9.09091
103 3I8T LBT 9.14634
104 3A7R LAQ 9.19881
105 2GJ5 VD3 9.25926
106 4CS4 ANP 9.48905
107 4CS4 AXZ 9.48905
108 2J3M ATP 9.53757
109 2J3M PRI 9.53757
110 3HCH RSM 9.58904
111 3E9I XAH 9.70874
112 5NLD LBT 9.70874
113 1GP6 QUE 9.70874
114 1GP6 DH2 9.70874
115 1GP6 SIN 9.70874
116 2JIG PD2 9.70874
117 2E5A LAQ 9.70874
118 5J75 6GQ 9.70874
119 3ZXE PGZ 9.77444
120 6BYM HC3 9.85222
121 5TBM 79A 10.2564
122 2BOS GLA GAL GLC 10.2941
123 2BOS GLA GAL 10.2941
124 3G1Z AMP 10.6796
125 1X54 4AD 10.6796
126 3MTX PGT 10.6796
127 2VFT SOR 10.6796
128 5T7I LAT NAG GAL 10.6796
129 2Z3U CRR 10.6796
130 1DZK PRZ 10.6796
131 2X34 UQ8 10.6796
132 3VSV XYP 10.6796
133 5ML3 DL3 11.4094
134 1WLE SRP 11.6505
135 4RF7 ARG 11.6505
136 3QRC SCR 11.6505
137 5XIJ ANP 11.6505
138 5XIJ 873 11.6505
139 2XMY CDK 11.6505
140 4QXB OGA 11.6505
141 1HXD BTN 11.6505
142 1E1O LYS 12.6214
143 3ERR AMP 12.6214
144 5G48 1FL 12.6214
145 4IAW LIZ 12.6214
146 5K21 6QF 12.766
147 4WVW SLT 13.1944
148 2FVK DUC 13.2948
149 1I7E IBS 13.5849
150 4YDQ HFG 13.5922
151 4YDQ ANP 13.5922
152 6CLV 6MB 13.5922
153 4HWS 1B3 13.8728
154 3WUD GLC GAL 13.9706
155 3VV1 GAL FUC 14.375
156 3A5Z KAA 14.5631
157 5XIO ANP 14.5631
158 3IAL PR8 16.5049
159 4PSB GA3 17.4757
160 4WOE ADP 18.4466
161 4NG2 OHN 18.5841
162 5H9P TD2 19.4175
163 5HV7 RBL 20.3883
164 4J36 1HR 20.3883
165 2G30 ALA ALA PHE 20.3883
166 12AS AMP 21.3592
167 1YFS ALA 21.3592
168 1YUM NCN 21.3592
169 6CB2 OLC 21.3592
170 3WG3 A2G GAL NAG FUC 21.9101
171 3A5Y KAA 22.3301
172 3B00 16A 22.3301
173 3QO8 SSA 22.8324
174 5H9Q TD2 23.2258
175 1KGI T4A 23.622
176 1WW5 SGA BGC 24.375
177 3VQ2 LP4 LP5 MYR DAO 25
178 1SDW IYT 25.2427
179 2CJA ATP 26.2136
180 3UH0 TSB 27.1845
181 5V59 8X1 28.1553
182 1ERB ETR 29.1262
183 2CJ9 SSA 30.0578
184 2I4O ATP 33.0097
185 2IUW AKG 37.8641
Pocket No.: 2; Query (leader) PDB : 4H2X; Ligand: G5A; Similar sites found with APoc: 49
This union binding pocket(no: 2) in the query (biounit: 4h2x.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 4TWL ASC 0.813008
2 5ODY 9SK 2.17391
3 4Z3E GAL NGA GLA BGC GAL 3.0303
4 4MVK ACE VAL PHE PHE ALA GLU ASP NH2 3.19149
5 2BS5 BGC GAL FUC 3.33333
6 5JNN 6LM 3.68421
7 5F2T PLM 3.8835
8 3DLG GWE 4.85437
9 5DYO FLU 4.85437
10 5LRT ADP 5.78035
11 5Y72 DST 5.82524
12 4DQ2 BTX 5.82524
13 5A6N U7E 5.82524
14 4WW8 VD9 6.46388
15 1VA6 ADP 6.6474
16 1VA6 P2S 6.6474
17 1DCP HBI 6.73077
18 3E85 BSU 6.79612
19 3FP0 FP0 6.79612
20 3E8N VRA 6.79612
21 3E8N ATP 6.79612
22 1WPY BTN 6.80851
23 4HIA FMN 6.81818
24 5DRB 5FJ 7.2165
25 4XTX 590 7.76699
26 3EFS BTN 7.76699
27 3PVW QRX 8.10811
28 1UNB AKG 8.73786
29 2QCS ANP 8.73786
30 3FHI ANP 8.73786
31 4IMO PWZ 9.70874
32 5DQ8 FLF 10.4167
33 2YAB AMP 10.6796
34 3IES M24 10.6796
35 5KD6 6C7 10.6936
36 3L9R L9Q 11.2245
37 4XMF HSM 11.6505
38 4HVA 4HV 12.6214
39 3ORK AGS 12.6214
40 5EO8 TFU 13.5922
41 5D9G GLU ASN LEU TYR PHE GLN 13.5922
42 3WW2 SF9 15.534
43 1TT8 PHB 16.5049
44 6B3V 7DQ 18.4466
45 6B3V ANP 18.4466
46 4ZOH FAD 22.3301
47 2RHQ GAX 24.2718
48 4WB6 ATP 30
49 4WB7 ATP 30
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