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: 250
No: Ligand ECFP6 Tc MDL keys Tc
1 G5A 1 1
2 A5A 0.746988 0.940476
3 SSA 0.738095 0.97619
4 VMS 0.729412 0.918605
5 52H 0.729412 0.908046
6 54H 0.729412 0.918605
7 NSS 0.724138 0.952941
8 DSZ 0.724138 0.952941
9 5AS 0.721519 0.930233
10 53H 0.72093 0.908046
11 TSB 0.72093 0.929412
12 5CA 0.72093 0.97619
13 LSS 0.704545 0.931035
14 KAA 0.7 0.965116
15 NVA LMS 0.696629 0.909091
16 LEU LMS 0.688889 0.909091
17 P5A 0.681319 0.954023
18 GSU 0.681319 0.952941
19 4YB 0.670103 0.931035
20 YSA 0.645833 0.952941
21 649 0.643564 0.910112
22 AMP 0.604938 0.776471
23 A 0.604938 0.776471
24 SRA 0.597561 0.802326
25 WSA 0.596154 0.964286
26 SON 0.593023 0.793103
27 AMP MG 0.590361 0.738636
28 CA0 0.586207 0.781609
29 A2D 0.583333 0.77907
30 ABM 0.583333 0.758621
31 5N5 0.578947 0.714286
32 ADN 0.573333 0.714286
33 RAB 0.573333 0.714286
34 XYA 0.573333 0.714286
35 GAP 0.571429 0.802326
36 AOC 0.571429 0.697674
37 5CD 0.571429 0.682353
38 AP2 0.569767 0.772727
39 A12 0.569767 0.772727
40 BA3 0.569767 0.77907
41 AU1 0.568182 0.781609
42 ADX 0.568182 0.894118
43 B4P 0.563218 0.77907
44 ADP 0.563218 0.77907
45 AP5 0.563218 0.77907
46 50T 0.561798 0.75
47 3DH 0.560976 0.678161
48 AN2 0.556818 0.790698
49 APR 0.555556 0.77907
50 AR6 0.555556 0.77907
51 A3G 0.552941 0.761905
52 A4D 0.551282 0.714286
53 M33 0.550562 0.770115
54 ADP MG 0.550562 0.75
55 SAP 0.549451 0.804598
56 AGS 0.549451 0.804598
57 ADV 0.549451 0.772727
58 RBY 0.549451 0.772727
59 5AL 0.548387 0.790698
60 ACP 0.544444 0.781609
61 ATP 0.544444 0.77907
62 ADP BEF 0.544444 0.733333
63 5X8 0.544444 0.729412
64 BEF ADP 0.544444 0.733333
65 SLU 0.54386 0.897727
66 DTA 0.54321 0.709302
67 AHX 0.540816 0.827586
68 TXA 0.54 0.772727
69 5FA 0.538462 0.77907
70 PRX 0.538462 0.741573
71 AQP 0.538462 0.77907
72 APC 0.538462 0.772727
73 ANP 0.537634 0.781609
74 SRP 0.536842 0.835294
75 AD9 0.532609 0.761364
76 ADP PO3 0.532609 0.776471
77 EP4 0.530864 0.662921
78 4AD 0.530612 0.804598
79 AMO 0.530612 0.813953
80 ATP MG 0.526882 0.75
81 DAL AMP 0.525773 0.770115
82 DLL 0.525253 0.790698
83 NB8 0.524752 0.806818
84 M2T 0.52439 0.666667
85 6RE 0.523256 0.707865
86 ACQ 0.521277 0.781609
87 TAT 0.521277 0.793103
88 ANP MG 0.520833 0.764045
89 ADP VO4 0.520833 0.770115
90 VO4 ADP 0.520833 0.770115
91 8QN 0.520408 0.790698
92 OOB 0.520408 0.790698
93 3UK 0.52 0.781609
94 MTA 0.518072 0.678161
95 DSH 0.517241 0.715909
96 PAJ 0.515152 0.758242
97 ADQ 0.515152 0.781609
98 LAD 0.514852 0.818182
99 J7C 0.511364 0.715909
100 A3N 0.511364 0.689655
101 ADP ALF 0.510417 0.725275
102 ATF 0.510417 0.752809
103 ALF ADP 0.510417 0.725275
104 MAP 0.510204 0.764045
105 A22 0.510204 0.770115
106 00A 0.51 0.755556
107 3OD 0.509804 0.781609
108 S4M 0.505618 0.680851
109 GJV 0.505618 0.7
110 25A 0.50505 0.77907
111 5SV 0.50505 0.709677
112 OAD 0.504951 0.781609
113 XAH 0.504762 0.820225
114 7MD 0.504673 0.820225
115 SA8 0.5 0.681319
116 9SN 0.5 0.747253
117 WAQ 0.5 0.775281
118 PR8 0.5 0.808989
119 PTJ 0.495146 0.747253
120 1ZZ 0.495146 0.723404
121 ME8 0.495146 0.78022
122 SAH 0.494737 0.712644
123 SFG 0.494624 0.697674
124 ZAS 0.494253 0.712644
125 MYR AMP 0.490385 0.705263
126 ADP BMA 0.490196 0.761364
127 A1R 0.485149 0.816092
128 EEM 0.484536 0.648936
129 MAO 0.483516 0.728261
130 NEC 0.483146 0.674419
131 ARG AMP 0.481818 0.771739
132 7C5 0.481481 0.7
133 FA5 0.481132 0.813953
134 YAP 0.481132 0.804598
135 SXZ 0.480769 0.684783
136 BIS 0.480769 0.736264
137 SAI 0.479167 0.685393
138 YLP 0.477477 0.782609
139 TYR AMP 0.476636 0.772727
140 25L 0.47619 0.770115
141 594 0.475 0.833333
142 SMM 0.474747 0.680851
143 S7M 0.474747 0.684783
144 SAM 0.474227 0.684783
145 6V0 0.473214 0.766667
146 A7D 0.473118 0.72093
147 TAD 0.472727 0.777778
148 AMP DBH 0.472222 0.722222
149 4UV 0.472222 0.764045
150 A A 0.471154 0.758621
151 LAQ 0.468468 0.76087
152 5AD 0.468354 0.630952
153 MHZ 0.468085 0.691489
154 JB6 0.466667 0.795455
155 FYA 0.466667 0.790698
156 3AM 0.465909 0.764706
157 7MC 0.464912 0.802198
158 YLB 0.464912 0.782609
159 LPA AMP 0.464286 0.741935
160 48N 0.464286 0.766667
161 4UU 0.463636 0.764045
162 AR6 AR6 0.463636 0.758621
163 GEK 0.460784 0.727273
164 DND 0.460177 0.772727
165 NAX 0.460177 0.769231
166 NXX 0.460177 0.772727
167 A3S 0.457447 0.75
168 0UM 0.456311 0.692308
169 LA8 ALF 3PG 0.45614 0.73913
170 AF3 ADP 3PG 0.45614 0.73913
171 OMR 0.45614 0.715789
172 TXE 0.45614 0.775281
173 ALF ADP 3PG 0.45614 0.73913
174 AHZ 0.455357 0.723404
175 AAT 0.454545 0.7
176 ATP A A A 0.453704 0.767442
177 A5D 0.453608 0.709302
178 YLC 0.452174 0.8
179 A2P 0.451613 0.764706
180 A3P 0.451613 0.776471
181 AFH 0.45045 0.758242
182 67D 0.449153 0.909091
183 A3T 0.447917 0.717647
184 K15 0.447619 0.659574
185 NAI 0.447368 0.755556
186 4UW 0.447368 0.73913
187 TXD 0.447368 0.775281
188 Y3J 0.445783 0.616279
189 7D7 0.444444 0.651163
190 IOT 0.444444 0.774194
191 V3L 0.444444 0.77907
192 TYM 0.443478 0.813953
193 7D5 0.443182 0.727273
194 COD 0.441667 0.776596
195 G3A 0.441441 0.747253
196 YLA 0.440678 0.782609
197 2AM 0.438202 0.755814
198 62X 0.438095 0.645833
199 G5P 0.4375 0.747253
200 AYB 0.436975 0.774194
201 CNA 0.436975 0.793103
202 UP5 0.434783 0.764045
203 590 0.434109 0.84375
204 GTA 0.433628 0.723404
205 NAD IBO 0.433333 0.744444
206 NAJ PZO 0.430894 0.747253
207 NAD 0.429752 0.790698
208 4TC 0.42735 0.766667
209 UPA 0.42735 0.775281
210 A2R 0.427184 0.770115
211 BT5 0.42623 0.755319
212 DZD 0.42623 0.777778
213 PPS 0.425743 0.872093
214 BS5 0.425 0.83871
215 ATR 0.424242 0.755814
216 PAP 0.424242 0.767442
217 YLY 0.424 0.774194
218 OVE 0.423913 0.770115
219 A4P 0.423729 0.747368
220 3AD 0.423529 0.722892
221 A3D 0.422764 0.781609
222 KB1 0.422018 0.673913
223 A6D 0.420561 0.677419
224 S8M 0.419048 0.727273
225 2VA 0.418367 0.701149
226 BTX 0.418033 0.763441
227 139 0.416667 0.769231
228 T5A 0.416667 0.744681
229 3NZ 0.416667 0.727273
230 AP0 0.415254 0.728261
231 2A5 0.414141 0.761364
232 N0B 0.414062 0.782609
233 M24 0.412698 0.75
234 7D3 0.410526 0.730337
235 CC5 0.409639 0.710843
236 D3Y 0.409524 0.732558
237 NAE 0.409449 0.764045
238 KH3 0.408696 0.670213
239 7D4 0.408163 0.730337
240 4TA 0.406504 0.734043
241 NAJ PYZ 0.40625 0.75
242 NAQ 0.40625 0.747253
243 SO8 0.405941 0.693182
244 VRT 0.405941 0.715909
245 ADJ 0.404959 0.734043
246 J1D 0.403226 0.728155
247 ZID 0.403101 0.781609
248 AMP NAD 0.403101 0.752809
249 IMO 0.4 0.744186
250 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: 78
This union binding pocket(no: 1) in the query (biounit: 4h2x.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3OJI PYV 0.005003 0.40833 2.6455
2 3ZJX BOG 0.009134 0.42642 2.76817
3 4O9S 2RY 0.01029 0.40278 2.7907
4 2XGT NSS 0.0000002083 0.6135 3.67816
5 3REU ATP 0.0000004319 0.57271 3.7415
6 1MDC PLM 0.0007674 0.4475 3.78788
7 3NEM AMO 0.0000001285 0.6204 3.8835
8 3NEM ATP 0.000001211 0.51828 3.8835
9 3TEG DAH 0.0007483 0.44604 3.8835
10 4WVO 3UZ 0.01075 0.40335 3.8835
11 3CH6 NAP 0.0369 0.40144 3.8835
12 3CH6 311 0.0369 0.40144 3.8835
13 3D91 REM 0.0463 0.40045 4.04624
14 2ZHL NAG GAL GAL NAG 0.01021 0.40734 4.05405
15 3L5R 47X 0.02618 0.42317 4.09836
16 4AZP A9M 0.007848 0.40495 4.85437
17 3DLG GWE 0.04276 0.40278 4.85437
18 4HWT 1B2 0.00011 0.47763 4.91329
19 4JH6 FCN 0.02102 0.40018 5.7971
20 3HXU A5A 0.00000006813 0.6245 5.82524
21 3LVW GSH 0.006067 0.42463 5.82524
22 5XDT MB3 0.01178 0.40909 5.82524
23 5DEY 59T 0.03482 0.40126 5.82524
24 1QY1 PRZ 0.001774 0.42975 6.32184
25 5VAD 91Y 0.00000701 0.5531 6.35838
26 2ZTG A5A 0.0000001001 0.61614 6.79612
27 1R5L VIV 0.005736 0.41255 6.79612
28 5DMZ ADP 0.003769 0.40733 6.79612
29 2DXU BT5 0.01379 0.40363 6.80851
30 4HIA FMN 0.01013 0.41325 6.81818
31 1B7Y FYA 0.000002054 0.567 7.76699
32 3T4L ZEA 0.00111 0.42945 7.76699
33 4XTX 590 0.01152 0.40337 7.76699
34 1SES AHX 0.0000001567 0.61584 7.83848
35 1SES AMP 0.000003185 0.58916 7.83848
36 3IX8 TX3 0.004696 0.41794 8.09249
37 3BJU ATP 0.00001112 0.50074 8.3815
38 1G51 AMO 0.000004174 0.55547 8.73786
39 3G08 FEE 0.01611 0.41898 9.09091
40 3A7R LAQ 0.01741 0.40345 9.19881
41 4CS4 ANP 0.0000001691 0.6379 9.48905
42 4CS4 AXZ 0.0000002758 0.63765 9.48905
43 2J3M PRI 0.0000001945 0.6073 9.53757
44 2J3M ATP 0.0000002445 0.60026 9.53757
45 3E9I XAH 0.0000003044 0.61065 9.70874
46 1GP6 QUE 0.006063 0.41301 9.70874
47 1GP6 SIN 0.006576 0.40992 9.70874
48 1GP6 DH2 0.006576 0.40992 9.70874
49 2E5A LAQ 0.01127 0.4038 9.70874
50 4XT2 43L 0.003318 0.4197 9.91736
51 1X54 4AD 0.0000004498 0.59384 10.6796
52 3G1Z AMP 0.0000006357 0.53076 10.6796
53 3MTX PGT 0.00248 0.43751 10.6796
54 1DZK PRZ 0.00158 0.41145 10.6796
55 2X34 UQ8 0.02971 0.40158 10.6796
56 5ML3 DL3 0.017 0.40497 11.4094
57 1WLE SRP 0.0000004511 0.58006 11.6505
58 2XMY CDK 0.02363 0.4162 11.6505
59 1E1O LYS 0.0000008736 0.58347 12.6214
60 3ERR AMP 0.000009114 0.49555 12.6214
61 4IAW LIZ 0.001643 0.40106 12.6214
62 4YDQ ANP 0.00002466 0.55253 13.5922
63 4YDQ HFG 0.00002339 0.55253 13.5922
64 4HWS 1B3 0.0000002947 0.46507 13.8728
65 3A5Z KAA 0.000000844 0.58414 14.5631
66 3IAL PR8 0.00000165 0.56404 16.5049
67 4PSB GA3 0.01724 0.40149 17.4757
68 4NG2 OHN 0.00868 0.40457 18.5841
69 12AS AMP 0.00003983 0.51181 21.3592
70 3A5Y KAA 0.0000001621 0.6134 22.3301
71 3QO8 SSA 0.0000001262 0.62005 22.8324
72 1KGI T4A 0.001888 0.43219 23.622
73 3VQ2 LP4 LP5 MYR DAO 0.0261 0.40094 25
74 2CJA ATP 0.000001106 0.5476 26.2136
75 3UH0 TSB 0.0000000772 0.62493 27.1845
76 1ERB ETR 0.007785 0.40962 29.1262
77 2CJ9 SSA 0.000000004526 0.66583 30.0578
78 2I4O ATP 0.000000367 0.5384 33.0097
Pocket No.: 2; Query (leader) PDB : 4H2X; Ligand: G5A; 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: 4h2x.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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