-->
Receptor
PDB id Resolution Class Description Source Keywords
2QUJ 2.42 Å EC: 6.1.1.2 CRYSTAL STRUCTURES OF HUMAN TRYPTOPHANYL-TRNA SYNTHETASE IN WITH TRPAMP HOMO SAPIENS AMINOACYL-TRNA SYNTHETASE ROSSMANN FOLD INDUCED-FIT MECHNIBINDING LIGASE NUCLEOTIDE-BINDING PROTEIN BIOSYNTHESIS
Ref.: CATALYTIC MECHANISM OF THE TRYPTOPHAN ACTIVATION RE REVEALED BY CRYSTAL STRUCTURES OF HUMAN TRYPTOPHANY SYNTHETASE IN DIFFERENT ENZYMATIC STATES NUCLEIC ACIDS RES. V. 36 1288 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:802;
A:804;
A:805;
A:807;
A:809;
B:801;
B:803;
B:806;
B:808;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
35.453 Cl [Cl-]
GOL A:813;
A:814;
B:812;
B:815;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
TRP B:817;
Valid;
none;
submit data
204.225 C11 H12 N2 O2 c1ccc...
TYM A:810;
Valid;
none;
submit data
533.431 C21 H24 N7 O8 P c1ccc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1R6T 2.1 Å EC: 6.1.1.2 CRYSTAL STRUCTURE OF HUMAN TRYPTOPHANYL-TRNA SYNTHETASE HOMO SAPIENS CLASS IC TRNA SYNTHETASE ROSSMANN FOLD CATALYTICAL DOMAIN RECOGNITION DOMAIN BOUND TRP-AMP LIGASE
Ref.: CRYSTAL STRUCTURES THAT SUGGEST LATE DEVELOPMENT OF CODE COMPONENTS FOR DIFFERENTIATING AROMATIC SIDE C PROC.NATL.ACAD.SCI.USA V. 100 15376 2003
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 5UJJ - TYM C21 H24 N7 O8 P c1ccc2c(c1....
2 2QUI - LTN C11 H13 N3 O c1ccc2c(c1....
3 1R6T - TYM C21 H24 N7 O8 P c1ccc2c(c1....
4 2QUJ - TRP C11 H12 N2 O2 c1ccc2c(c1....
5 2QUH - TRP C11 H12 N2 O2 c1ccc2c(c1....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1R6U - TYM C21 H24 N7 O8 P c1ccc2c(c1....
2 5UJJ - TYM C21 H24 N7 O8 P c1ccc2c(c1....
3 2QUI - LTN C11 H13 N3 O c1ccc2c(c1....
4 1R6T - TYM C21 H24 N7 O8 P c1ccc2c(c1....
5 2QUJ - TRP C11 H12 N2 O2 c1ccc2c(c1....
6 2QUH - TRP C11 H12 N2 O2 c1ccc2c(c1....
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 1R6U - TYM C21 H24 N7 O8 P c1ccc2c(c1....
2 4J75 - TYM C21 H24 N7 O8 P c1ccc2c(c1....
3 5UJJ - TYM C21 H24 N7 O8 P c1ccc2c(c1....
4 2QUI - LTN C11 H13 N3 O c1ccc2c(c1....
5 1R6T - TYM C21 H24 N7 O8 P c1ccc2c(c1....
6 2QUJ - TRP C11 H12 N2 O2 c1ccc2c(c1....
7 2QUH - TRP C11 H12 N2 O2 c1ccc2c(c1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TRP; Similar ligands found: 29
No: Ligand ECFP6 Tc MDL keys Tc
1 DTR 1 1
2 TRP 1 1
3 LTN 0.765957 0.777778
4 TR7 0.666667 0.833333
5 3IL 0.666667 0.75
6 4Z9 0.666667 0.75
7 FT6 0.561404 0.888889
8 IAC 0.538462 0.787879
9 TSR 0.529412 0.722222
10 IOP 0.518519 0.764706
11 R59 0.515152 0.72093
12 R38 0.515152 0.72093
13 3IB 0.491228 0.742857
14 ITW 0.491228 0.694444
15 IAD 0.484375 0.738095
16 TRP GLY 0.476923 0.704545
17 TSS 0.471698 0.666667
18 CTE 0.467742 0.888889
19 DTE 0.467742 0.888889
20 IAV 0.461538 0.738095
21 IAG 0.459016 0.738095
22 LYS TRP 0.432432 0.673913
23 78U 0.42623 0.794118
24 0ZN 0.421687 0.673913
25 4OG 0.416667 0.8
26 X95 0.411765 0.680851
27 LSW 0.411765 0.680851
28 ASP TRP ASN 0.405063 0.673913
29 GLU ASP ASN ASP TRP ASN 0.405063 0.673913
Ligand no: 2; Ligand: TYM; Similar ligands found: 244
No: Ligand ECFP6 Tc MDL keys Tc
1 TYM 1 1
2 FA5 0.72381 1
3 SRP 0.7 0.972973
4 YAP 0.691589 0.986486
5 AMO 0.673077 0.972973
6 LAD 0.669811 0.923077
7 WSA 0.666667 0.845238
8 5AL 0.663366 0.945946
9 ME8 0.648148 0.9
10 NB8 0.648148 0.935065
11 8QN 0.632075 0.945946
12 PAJ 0.626168 0.875
13 CA0 0.62 0.933333
14 4AD 0.611111 0.96
15 DLL 0.605505 0.972603
16 PTJ 0.603604 0.886076
17 OOB 0.601852 0.972603
18 YLP 0.59322 0.878049
19 A2D 0.585859 0.932432
20 3UK 0.585586 0.959459
21 WAQ 0.580357 0.922078
22 B5V 0.580357 0.946667
23 YLB 0.578512 0.878049
24 YLC 0.578512 0.9
25 AN2 0.578431 0.894737
26 AHX 0.576577 0.910256
27 BA3 0.574257 0.932432
28 AYB 0.572581 0.86747
29 AP5 0.568627 0.932432
30 B4P 0.568627 0.932432
31 ADP 0.568627 0.906667
32 YLA 0.564516 0.878049
33 AT4 0.563107 0.871795
34 00A 0.5625 0.922078
35 AR6 0.561905 0.932432
36 PRX 0.561905 0.858974
37 APR 0.561905 0.932432
38 1ZZ 0.561404 0.853659
39 FYA 0.561404 0.945946
40 ANP 0.560748 0.883117
41 B5M 0.560345 0.934211
42 ADX 0.557692 0.819277
43 M33 0.557692 0.894737
44 AD9 0.556604 0.883117
45 AMP 0.555556 0.905405
46 XAH 0.555556 0.876543
47 A 0.555556 0.905405
48 PR8 0.552632 0.911392
49 HEJ 0.552381 0.906667
50 ATP 0.552381 0.906667
51 ACP 0.552381 0.907895
52 50T 0.552381 0.87013
53 9SN 0.551724 0.910256
54 TXA 0.547826 0.921053
55 5FA 0.54717 0.906667
56 AQP 0.54717 0.906667
57 B5Y 0.547009 0.934211
58 SAP 0.542056 0.860759
59 AGS 0.542056 0.860759
60 YLY 0.541985 0.86747
61 A1R 0.539823 0.897436
62 ABM 0.539216 0.881579
63 3OD 0.534483 0.933333
64 ACQ 0.53211 0.907895
65 9ZA 0.530973 0.897436
66 25A 0.530973 0.932432
67 9ZD 0.530973 0.897436
68 N0B 0.529851 0.901235
69 AP2 0.528846 0.896104
70 A12 0.528846 0.896104
71 AU1 0.528302 0.883117
72 4UV 0.525 0.934211
73 V1N 0.525 0.932432
74 DQV 0.52459 0.945946
75 ATF 0.522523 0.871795
76 A22 0.522124 0.92
77 DAL AMP 0.522124 0.92
78 LAQ 0.520325 0.853659
79 SRA 0.519608 0.858974
80 GAP 0.518182 0.907895
81 6YZ 0.517857 0.907895
82 OAD 0.517241 0.933333
83 ADV 0.513761 0.921053
84 RBY 0.513761 0.921053
85 A3R 0.513043 0.897436
86 TXE 0.507937 0.897436
87 M24 0.507463 0.8875
88 SON 0.504673 0.946667
89 APC 0.504587 0.896104
90 TAT 0.504505 0.871795
91 T99 0.504505 0.871795
92 5SV 0.504348 0.817073
93 9X8 0.504274 0.884615
94 25L 0.504202 0.92
95 4UU 0.504065 0.934211
96 BT5 0.5 0.86747
97 ADQ 0.5 0.933333
98 NAI 0.5 0.897436
99 DND 0.5 0.946667
100 NXX 0.5 0.946667
101 4UW 0.5 0.898734
102 TYR AMP 0.5 0.96
103 80F 0.496241 0.901235
104 IOT 0.496124 0.86747
105 7MD 0.491935 0.9
106 NAX 0.488189 0.911392
107 TXD 0.488189 0.897436
108 AMP DBH 0.487805 0.883117
109 ADP PO3 0.486486 0.905405
110 G3A 0.483871 0.886076
111 BIS 0.483333 0.85
112 MAP 0.482759 0.860759
113 ADP ALF 0.482456 0.8375
114 ALF ADP 0.482456 0.8375
115 T5A 0.480916 0.878049
116 48N 0.480315 0.910256
117 G5P 0.48 0.886076
118 VO4 ADP 0.478261 0.894737
119 ADP VO4 0.478261 0.894737
120 SSA 0.478261 0.813953
121 6V0 0.476562 0.886076
122 LSS 0.474576 0.795455
123 F2R 0.473684 0.878049
124 NAE 0.471014 0.909091
125 NAD 0.470149 0.945946
126 TSB 0.470085 0.790698
127 5CA 0.470085 0.813953
128 A5A 0.469565 0.8
129 AP0 0.469231 0.8625
130 ARG AMP 0.468254 0.865854
131 AFH 0.468254 0.898734
132 GA7 0.468254 0.896104
133 YSA 0.467742 0.835294
134 NAQ 0.467626 0.886076
135 MYR AMP 0.467213 0.831325
136 LMS 0.466667 0.797619
137 CNA 0.466165 0.946667
138 BV8 0.465517 0.811111
139 GTA 0.464567 0.853659
140 A3D 0.463235 0.933333
141 KAA 0.46281 0.786517
142 A A 0.46281 0.906667
143 DSZ 0.462185 0.835294
144 54H 0.461538 0.781609
145 VMS 0.461538 0.781609
146 AF3 ADP 3PG 0.461538 0.875
147 OMR 0.461538 0.843373
148 BVT 0.460227 0.802198
149 PAP 0.460177 0.893333
150 COD 0.459259 0.825581
151 139 0.458647 0.8875
152 ADJ 0.458647 0.865854
153 UPA 0.458015 0.897436
154 AOC 0.457944 0.789474
155 53H 0.457627 0.772727
156 ADP BMA 0.454545 0.907895
157 UP5 0.453846 0.909091
158 2A5 0.451327 0.858974
159 GSU 0.45082 0.835294
160 BJW 0.45 0.820225
161 52H 0.449153 0.772727
162 RAB 0.44898 0.786667
163 ADN 0.44898 0.786667
164 XYA 0.44898 0.786667
165 AMP NAD 0.448529 0.945946
166 BTX 0.448529 0.855422
167 PPS 0.448276 0.797619
168 8PZ 0.448 0.835294
169 ATP A A A 0.448 0.918919
170 EAD 0.447552 0.8875
171 9K8 0.447154 0.747253
172 JB6 0.447154 0.897436
173 7MC 0.44697 0.878049
174 4TC 0.44697 0.910256
175 A3P 0.445455 0.905405
176 DZD 0.445255 0.898734
177 A4P 0.443609 0.835294
178 G5A 0.443478 0.813953
179 5X8 0.442478 0.826667
180 TAD 0.44186 0.875
181 5AS 0.441441 0.752809
182 NSS 0.438017 0.813953
183 0WD 0.437956 0.886076
184 A2R 0.436975 0.92
185 5CD 0.435644 0.773333
186 COT 0.435583 0.818182
187 NDE 0.435374 0.921053
188 P1H 0.435374 0.865854
189 LPA AMP 0.435115 0.831325
190 SA8 0.434783 0.765432
191 ATR 0.434783 0.88
192 NVA LMS 0.434426 0.786517
193 AR6 AR6 0.434109 0.932432
194 ZID 0.433566 0.933333
195 8X1 0.433333 0.786517
196 SAI 0.431034 0.794872
197 SAH 0.431034 0.805195
198 LEU LMS 0.430894 0.786517
199 CA3 0.430303 0.818182
200 SFG 0.429825 0.813333
201 SMM 0.428571 0.741176
202 NAJ PZO 0.428571 0.8625
203 AHZ 0.427481 0.831325
204 P5A 0.427419 0.777778
205 SAM 0.42735 0.746988
206 5N5 0.425743 0.763158
207 7D5 0.424528 0.820513
208 EEM 0.423729 0.746988
209 7D3 0.423423 0.822785
210 A4D 0.421569 0.763158
211 7D4 0.421053 0.822785
212 A2P 0.419643 0.891892
213 DTA 0.419048 0.779221
214 G A A A 0.417266 0.8625
215 4TA 0.417266 0.865854
216 3AM 0.416667 0.866667
217 V3L 0.415254 0.932432
218 6AD 0.411765 0.829268
219 ARU 0.41129 0.785714
220 NDC 0.410596 0.886076
221 FB0 0.410596 0.797753
222 A5D 0.410256 0.779221
223 NJP 0.410072 0.909091
224 EP4 0.409524 0.725
225 6RE 0.409091 0.753086
226 4YB 0.409091 0.837209
227 ITT 0.408696 0.855263
228 3DH 0.407407 0.74359
229 A G 0.407143 0.873418
230 NAJ PYZ 0.406897 0.821429
231 NDP 0.405797 0.886076
232 M2T 0.40566 0.707317
233 DCA 0.405594 0.816092
234 FDA 0.405229 0.825581
235 FNK 0.405063 0.818182
236 S7M 0.404959 0.746988
237 7C5 0.40458 0.833333
238 U A G G 0.404255 0.873418
239 67D 0.402878 0.795455
240 MTA 0.401869 0.74359
241 IMO 0.401786 0.866667
242 J7C 0.401786 0.7625
243 62X 0.4 0.72093
244 A3S 0.4 0.826667
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1R6T; Ligand: TYM; Similar sites found with APoc: 133
This union binding pocket(no: 1) in the query (biounit: 1r6t.bio1) has 39 residues
No: Leader PDB Ligand Sequence Similarity
1 5CLO NS8 None
2 4GR5 APC 1.04822
3 4OFJ HIS 1.05708
4 5D3U TRP 1.17096
5 1WD4 AHR 1.25786
6 5Y0N ATP 1.37931
7 5Y0Q APC 1.38249
8 1V47 ADX 1.43266
9 1F9V ADP 1.44092
10 3LE7 ADE 1.53257
11 4YMJ 4EJ 1.64474
12 5CJF 520 1.79211
13 1WTC ACP 1.85759
14 5DZT AMP 1.88679
15 4JBL MET 2.0649
16 2H29 DND 2.1164
17 5XLX SAH 2.12766
18 1KQN NAD 2.15054
19 2Z9I GLY ALA THR VAL 2.16049
20 3PD6 PMP 2.24439
21 1QPB PYM 2.30608
22 6E1Q CFA 2.30608
23 1H3F TYE 2.31481
24 3HYW DCQ 2.32558
25 6BSW UDP 2.36686
26 2X3F APC 2.45614
27 6GN6 MAL 2.46085
28 2GKS ADP 2.51572
29 3AFH GSU 2.51572
30 5EY0 GTP 2.55474
31 3CW9 AMP 2.57937
32 4ZEV M6P 2.7027
33 5L2R MLA 2.72537
34 1T36 ORN 2.72537
35 2AOT SAH 2.73973
36 1J09 ATP 2.77778
37 1J09 GLU 2.77778
38 5LLT DND 2.8169
39 2X1L ADN 2.93501
40 5ZDK ATP 2.93501
41 1GPM CIT 2.93501
42 4NFE BEN 2.95359
43 5XK9 DMA 3.01724
44 2QK4 ATP 3.09735
45 5X3D 7XL 3.125
46 1JZS MRC 3.14465
47 2V0C LEU LMS 3.14465
48 4FHT DHB 3.18471
49 5XET ME8 3.21361
50 1K4M NAD 3.28639
51 1K4M CIT 3.28639
52 5ZDN CDP 3.31754
53 3C8Z 5CA 3.38164
54 1DDU DDU 3.39623
55 5H5L GSH 3.46535
56 4D4U FUC GAL NAG 3.49206
57 2B8T THM 3.58744
58 2QTR NXX 3.7037
59 4MAF ADX 3.71287
60 1Z45 UPG 3.77358
61 4IF4 BEF 3.84615
62 1N1D C2G 3.87597
63 1MJT ITU 4.03458
64 1Y7P RIP 4.03587
65 1Y42 TYR 4.08163
66 5AHO TLA 4.16667
67 4AG9 COA 4.24242
68 5CX8 TG6 4.40252
69 6C0B MLI 4.48718
70 2RBK VN4 4.5977
71 4BJH PAL 4.60526
72 3COW 52H 4.65116
73 3QXV MTX 4.7619
74 5WZU 7W3 4.87805
75 2YYE APC 4.92754
76 5OFW 9TW 4.93274
77 1G4U AF3 4.96084
78 4TVD BGC 5.24109
79 1O6B ADP 5.32544
80 4URN NOV 5.33333
81 1YUM NCN 5.3719
82 5O0B 9FE 5.55556
83 5N53 8NB 5.64103
84 1L7N ALF 5.6872
85 1L7P SEP 5.6872
86 1L7N AF3 5.6872
87 3UC5 ATP 5.73248
88 5F90 GLA GAL 5.76923
89 5YRV 5AD 5.83942
90 3WR7 COA 5.88235
91 1SQL GUN 6.07966
92 2FT0 ACO 6.38298
93 5V49 8WA 6.49895
94 5W3Y ACO 6.53409
95 3ZIU LSS 6.7086
96 3HL4 CDC 6.77966
97 2NZU BG6 6.78571
98 5Y0T TAT 6.82353
99 1PFY MSP 6.91824
100 2X9L BOG 6.95971
101 3HAV SRY 7.02341
102 1X8X TYR 7.14286
103 4TS1 TYR 7.21003
104 2PID YSA 7.54717
105 3Q8U ADP 7.64331
106 2QIE 8CS 7.79221
107 3LQV ADE 7.82609
108 4L6T GAL NGA GAL BGC SIA 8.03571
109 2YN4 39J 8.05085
110 1PFK ADP 8.125
111 1JIL 485 8.33333
112 3KFL ME8 8.80503
113 4U60 SIA GAL NGA 9.28571
114 4U60 SIA 9.28571
115 2VT3 ATP 9.30233
116 4R57 ACO 9.65909
117 5WBF LAC 10.3704
118 3BQF SSM 11.3402
119 3QX9 ATP 11.5942
120 3H0L ADP 11.7021
121 1MFI FHC 12.2807
122 2W9S TOP 13.0435
123 1F9A ATP 13.0952
124 5HQ0 LZ9 13.245
125 2NZ2 CIR 13.3172
126 1L5Y BEF 14.1935
127 2JEN GLC GLC XYS XYS 17.2414
128 1Q11 TYE 19.6237
129 2J5B TYE 20.977
130 2CYC TYR 25.0667
131 5N5U AMP 36.6242
132 5N5U 7N8 36.6242
133 2CYB TYR 40.2477
APoc FAQ
Feedback