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Receptor
PDB id Resolution Class Description Source Keywords
4J75 2.4 Å EC: 6.1.1.2 CRYSTAL STRUCTURE OF A PARASITE TRNA SYNTHETASE, PRODUCT-BOU PLASMODIUM FALCIPARUM AMINOACYL-TRNA SYNTHETASE AARS TRPRS PARASITE PROTEIN-SUCOMPLEX ROSSMANN FOLD TRANSLATION NUCLEOTIDE BINDING LI
Ref.: CRYSTAL STRUCTURES OF PLASMODIUM FALCIPARUM CYTOSOL TRYPTOPHANYL-TRNA SYNTHETASE AND ITS POTENTIAL AS A FOR STRUCTURE-GUIDED DRUG DESIGN. MOL.BIOCHEM.PARASITOL. V. 189 26 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:703;
A:702;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
TYM B:701;
A:701;
Valid;
Valid;
none;
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
4J75 2.4 Å EC: 6.1.1.2 CRYSTAL STRUCTURE OF A PARASITE TRNA SYNTHETASE, PRODUCT-BOU PLASMODIUM FALCIPARUM AMINOACYL-TRNA SYNTHETASE AARS TRPRS PARASITE PROTEIN-SUCOMPLEX ROSSMANN FOLD TRANSLATION NUCLEOTIDE BINDING LI
Ref.: CRYSTAL STRUCTURES OF PLASMODIUM FALCIPARUM CYTOSOL TRYPTOPHANYL-TRNA SYNTHETASE AND ITS POTENTIAL AS A FOR STRUCTURE-GUIDED DRUG DESIGN. MOL.BIOCHEM.PARASITOL. V. 189 26 2013
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4J75 - TYM C21 H24 N7 O8 P c1ccc2c(c1....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 4J75 - TYM C21 H24 N7 O8 P 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: 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 : 4J75; Ligand: TYM; Similar sites found with APoc: 127
This union binding pocket(no: 1) in the query (biounit: 4j75.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 1J09 GLU 1.22249
2 1J09 ATP 1.22249
3 2QK4 ATP 1.46699
4 3G2Y GF4 1.52091
5 5C9P FUC 1.5748
6 3ZIU LSS 1.71149
7 2V0C LEU LMS 1.71149
8 4LHD GLY 1.95599
9 2YYE APC 2.02899
10 5JXZ ISC 2.04604
11 6BSW UDP 2.07101
12 3HL4 CDC 2.11864
13 1NLU IVA PHI TYB 2.16216
14 2F9W PAU 2.21402
15 5V59 8X1 2.31579
16 4PTN PYR 2.33236
17 2YFO GLA 2.44499
18 2YFO GAL 2.44499
19 2PZE ATP 2.62009
20 5XET ME8 2.68949
21 5DZT AMP 2.68949
22 1WB4 SXX 2.6936
23 2ZL7 FUC GAL NGA 2.71186
24 2X3F APC 2.80702
25 2ATJ BHO 2.92208
26 6GN6 MAL 2.93399
27 5Y0N ATP 2.98851
28 1MJT ITU 3.17003
29 5Y0T TAT 3.17848
30 5Y0Q APC 3.17848
31 4XFM THE 3.17848
32 5YSN 5AD 3.17848
33 5ZDK ATP 3.28467
34 1YUM NCN 3.30579
35 4Z7X 3CX 3.36134
36 4ZEV M6P 3.37838
37 3GUZ PAF 3.40909
38 4WOE 3S5 3.42298
39 1V47 ADX 3.4384
40 1O6B ADP 3.5503
41 1JZS MRC 3.66748
42 2ZTG A5A 3.66748
43 6CHP F0Y 3.72671
44 2YN4 39J 3.81356
45 1QB7 ADE 3.81356
46 1JPA ANP 3.84615
47 5WXU FLC 3.91198
48 4MAF ADX 3.9604
49 1SQL GUN 4.10959
50 3C8Z 5CA 4.15648
51 4TVD BGC 4.15648
52 3L8G GMB 4.27807
53 1MFI FHC 4.38596
54 1H3F TYE 4.40098
55 2BMB PMM 4.40098
56 1Y42 TYR 4.59184
57 2GKS ADP 4.64548
58 4C2C ALA ALA ALA 4.64548
59 4A91 GLU 4.69799
60 2W5P CL8 4.69799
61 2X1L ADN 4.88998
62 3COW 52H 4.88998
63 3R4S SLB 4.88998
64 4IF4 BEF 4.88998
65 1NXJ TLA 4.91803
66 5O0B 9FE 4.93827
67 2RBK VN4 4.98084
68 1CBK ROI 5
69 2PID YSA 5.05618
70 4O48 ASP 5.12048
71 6E1Q CFA 5.13447
72 2H29 DND 5.29101
73 3V0H I3P 5.30973
74 2JKG PRO PRO PRO PRO PRO PRO PRO PRO 5.58659
75 3EF0 ALF 5.62347
76 3HAV ATP 5.68562
77 3QX9 ATP 5.7971
78 3KFL ME8 5.86797
79 1KQN NAD 6.09319
80 1PFY MSP 6.11247
81 1N1D C2G 6.20155
82 5X3D 7XL 6.25
83 5OFW 9TW 6.27803
84 2QTR NXX 6.34921
85 2CBZ ATP 6.60147
86 3T4L ZEA 7.09046
87 5N53 8NB 7.17949
88 1ONI BEZ 7.97101
89 2OUA AES 7.97872
90 1HFE CYS 8.13008
91 1Q11 TYE 8.33333
92 3H0L ADP 8.51064
93 1RY2 AMP 8.55746
94 3FAL REA 8.67769
95 4NTO 1PW 8.69565
96 1YQC GLV 8.82353
97 3WR7 COA 8.82353
98 5LLT DND 8.92019
99 2F7A CCU 9.05172
100 4TS1 TYR 9.09091
101 1JIL 485 9.29095
102 1X8X TYR 9.31677
103 1K4M NAD 9.38967
104 4R57 ACO 10.2273
105 3AFH GSU 10.2689
106 5IJJ I6P 10.4167
107 5KK4 44E 10.4167
108 5YRV 5AD 10.5134
109 5TH5 MET 10.6464
110 5L2R MLA 11.0024
111 1F9A ATP 12.5
112 1M5W DXP 14.4033
113 1L5Y BEF 14.8387
114 2J5B TYE 14.9425
115 1ZX5 LFR 15.6667
116 2JEN GLC GLC XYS XYS 15.7088
117 1L7N ALF 16.1137
118 1L7P SEP 16.1137
119 1L7N AF3 16.1137
120 1GZF NIR 16.5877
121 5CIC 51R 16.6667
122 1DDU DDU 17.7358
123 5V49 8WA 18.0929
124 2CYC TYR 18.4
125 3LQV ADE 25.641
126 2CYB TYR 32.1981
127 5N5U AMP 35.3503
Pocket No.: 2; Query (leader) PDB : 4J75; Ligand: TYM; Similar sites found with APoc: 10
This union binding pocket(no: 2) in the query (biounit: 4j75.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 1SBR VIB 2
2 5JXZ ISJ 2.04604
3 3S6X SIA GAL BGC 2.46154
4 2XZ9 PYR 2.46914
5 3NIP 16D 3.06748
6 5LY1 PPI 4.19948
7 3E7S AT2 5.37897
8 4Q0P 0MK 5.76923
9 2RCU BUJ 8.55746
10 4USI AKG 9.09091
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