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 (6)
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 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....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TYM; Similar ligands found: 230
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 NB8 0.648148 0.935065
10 ME8 0.648148 0.9
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 YLC 0.578512 0.9
23 YLB 0.578512 0.878049
24 AN2 0.578431 0.894737
25 AHX 0.576577 0.910256
26 BA3 0.574257 0.932432
27 AYB 0.572581 0.86747
28 B4P 0.568627 0.932432
29 ADP 0.568627 0.906667
30 AP5 0.568627 0.932432
31 YLA 0.564516 0.878049
32 00A 0.5625 0.922078
33 PRX 0.561905 0.858974
34 AR6 0.561905 0.932432
35 APR 0.561905 0.932432
36 1ZZ 0.561404 0.853659
37 FYA 0.561404 0.945946
38 ANP 0.560748 0.883117
39 ADX 0.557692 0.819277
40 M33 0.557692 0.894737
41 AD9 0.556604 0.883117
42 XAH 0.555556 0.876543
43 AMP 0.555556 0.905405
44 A 0.555556 0.905405
45 PR8 0.552632 0.911392
46 ACP 0.552381 0.907895
47 ATP 0.552381 0.906667
48 50T 0.552381 0.87013
49 9SN 0.551724 0.910256
50 TXA 0.547826 0.921053
51 5FA 0.54717 0.906667
52 AQP 0.54717 0.906667
53 SAP 0.542056 0.860759
54 AGS 0.542056 0.860759
55 YLY 0.541985 0.86747
56 A1R 0.539823 0.897436
57 ABM 0.539216 0.881579
58 DAL AMP 0.535714 0.92
59 3OD 0.534483 0.933333
60 ACQ 0.53211 0.907895
61 25A 0.530973 0.932432
62 N0B 0.529851 0.901235
63 AMP MG 0.529412 0.857143
64 A12 0.528846 0.896104
65 AP2 0.528846 0.896104
66 AU1 0.528302 0.883117
67 4UV 0.525 0.934211
68 V1N 0.525 0.932432
69 ATF 0.522523 0.871795
70 A22 0.522124 0.92
71 LAQ 0.520325 0.853659
72 SRA 0.519608 0.858974
73 GAP 0.518182 0.907895
74 OAD 0.517241 0.933333
75 TYR AMP 0.516667 0.946667
76 ADV 0.513761 0.921053
77 RBY 0.513761 0.921053
78 TXE 0.507937 0.897436
79 M24 0.507463 0.8875
80 SON 0.504673 0.946667
81 APC 0.504587 0.896104
82 TAT 0.504505 0.871795
83 5SV 0.504348 0.817073
84 25L 0.504202 0.92
85 4UU 0.504065 0.934211
86 ADP MG 0.5 0.87013
87 NAI 0.5 0.897436
88 4UW 0.5 0.898734
89 DND 0.5 0.946667
90 ADQ 0.5 0.933333
91 NXX 0.5 0.946667
92 BT5 0.5 0.86747
93 IOT 0.496124 0.86747
94 BEF ADP 0.495413 0.848101
95 ADP BEF 0.495413 0.848101
96 7MD 0.491935 0.9
97 TXD 0.488189 0.897436
98 NAX 0.488189 0.911392
99 AMP DBH 0.487805 0.883117
100 ADP PO3 0.486486 0.905405
101 ARG AMP 0.484127 0.865854
102 G3A 0.483871 0.886076
103 BIS 0.483333 0.85
104 MAP 0.482759 0.860759
105 ALF ADP 0.482456 0.8375
106 ADP ALF 0.482456 0.8375
107 ATP MG 0.482143 0.87013
108 T5A 0.480916 0.878049
109 48N 0.480315 0.910256
110 G5P 0.48 0.886076
111 ANP MG 0.478261 0.860759
112 SSA 0.478261 0.813953
113 ADP VO4 0.478261 0.894737
114 VO4 ADP 0.478261 0.894737
115 6V0 0.476562 0.886076
116 LSS 0.474576 0.795455
117 NAE 0.471014 0.909091
118 NAD 0.470149 0.945946
119 5CA 0.470085 0.813953
120 TSB 0.470085 0.790698
121 A5A 0.469565 0.8
122 AP0 0.469231 0.8625
123 AFH 0.468254 0.898734
124 YSA 0.467742 0.835294
125 NAQ 0.467626 0.886076
126 MYR AMP 0.467213 0.831325
127 CNA 0.466165 0.946667
128 GTA 0.464567 0.853659
129 A3D 0.463235 0.933333
130 A A 0.46281 0.906667
131 KAA 0.46281 0.786517
132 DSZ 0.462185 0.835294
133 AF3 ADP 3PG 0.461538 0.875
134 54H 0.461538 0.781609
135 VMS 0.461538 0.781609
136 OMR 0.461538 0.843373
137 PAP 0.460177 0.893333
138 COD 0.459259 0.825581
139 ADJ 0.458647 0.865854
140 139 0.458647 0.8875
141 UPA 0.458015 0.897436
142 AOC 0.457944 0.789474
143 53H 0.457627 0.772727
144 ADP BMA 0.454545 0.907895
145 UP5 0.453846 0.909091
146 2A5 0.451327 0.858974
147 GSU 0.45082 0.835294
148 ALF ADP 3PG 0.450382 0.875
149 LA8 ALF 3PG 0.450382 0.875
150 52H 0.449153 0.772727
151 XYA 0.44898 0.786667
152 RAB 0.44898 0.786667
153 ADN 0.44898 0.786667
154 BTX 0.448529 0.855422
155 PPS 0.448276 0.797619
156 ATP A A A 0.448 0.918919
157 EAD 0.447552 0.8875
158 JB6 0.447154 0.897436
159 4TC 0.44697 0.910256
160 7MC 0.44697 0.878049
161 NVA LMS 0.446281 0.775281
162 A3P 0.445455 0.905405
163 DZD 0.445255 0.898734
164 A4P 0.443609 0.835294
165 G5A 0.443478 0.813953
166 LEU LMS 0.442623 0.775281
167 5X8 0.442478 0.826667
168 TAD 0.44186 0.875
169 5AS 0.441441 0.752809
170 NAD IBO 0.441176 0.884615
171 NSS 0.438017 0.813953
172 0WD 0.437956 0.886076
173 A2R 0.436975 0.92
174 5CD 0.435644 0.773333
175 COT 0.435583 0.818182
176 NDE 0.435374 0.921053
177 P1H 0.435374 0.865854
178 LPA AMP 0.435115 0.831325
179 ATR 0.434783 0.88
180 SA8 0.434783 0.765432
181 AR6 AR6 0.434109 0.932432
182 AMP NAD 0.433566 0.921053
183 ZID 0.433566 0.933333
184 SAI 0.431034 0.794872
185 SAH 0.431034 0.805195
186 CA3 0.430303 0.818182
187 SFG 0.429825 0.813333
188 SMM 0.428571 0.741176
189 NAJ PZO 0.428571 0.8625
190 AHZ 0.427481 0.831325
191 P5A 0.427419 0.777778
192 SAM 0.42735 0.746988
193 NAJ PYZ 0.426573 0.864198
194 5N5 0.425743 0.763158
195 7D5 0.424528 0.820513
196 EEM 0.423729 0.746988
197 7D3 0.423423 0.822785
198 A4D 0.421569 0.763158
199 7D4 0.421053 0.822785
200 A2P 0.419643 0.891892
201 DTA 0.419048 0.779221
202 4TA 0.417266 0.865854
203 G A A A 0.417266 0.8625
204 3AM 0.416667 0.866667
205 V3L 0.415254 0.932432
206 6AD 0.411765 0.829268
207 ARU 0.41129 0.785714
208 NDC 0.410596 0.886076
209 FB0 0.410596 0.797753
210 A5D 0.410256 0.779221
211 NJP 0.410072 0.909091
212 EP4 0.409524 0.725
213 4YB 0.409091 0.837209
214 6RE 0.409091 0.753086
215 ITT 0.408696 0.855263
216 3DH 0.407407 0.74359
217 NDP 0.405797 0.886076
218 M2T 0.40566 0.707317
219 DCA 0.405594 0.816092
220 FDA 0.405229 0.825581
221 FNK 0.405063 0.818182
222 S7M 0.404959 0.746988
223 7C5 0.40458 0.833333
224 U A G G 0.404255 0.873418
225 67D 0.402878 0.795455
226 MTA 0.401869 0.74359
227 J7C 0.401786 0.7625
228 IMO 0.401786 0.866667
229 A3S 0.4 0.826667
230 62X 0.4 0.72093
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4J75; Ligand: TYM; Similar sites found: 73
This union binding pocket(no: 1) in the query (biounit: 4j75.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1J09 GLU 0.0001177 0.43146 1.22249
2 1J09 ATP 0.0004612 0.40989 1.22249
3 2QK4 ATP 0.02363 0.40959 1.46699
4 3G2Y GF4 0.03585 0.40491 1.52091
5 3ZIU LSS 0.0000002178 0.58743 1.71149
6 2V0C LEU LMS 0.0000009602 0.56076 1.71149
7 2YYE APC 0.005917 0.40675 2.02899
8 3HL4 CDC 0.0002717 0.47177 2.11864
9 2F9W PAU 0.0332 0.4019 2.21402
10 4PTN PYR 0.03292 0.40672 2.33236
11 1WB4 SXX 0.02342 0.41457 2.6936
12 2ZL7 FUC GAL NGA 0.04424 0.40387 2.71186
13 2X3F APC 0.00005249 0.47222 2.80702
14 2ATJ BHO 0.008284 0.44284 2.92208
15 4WOE 3S5 0.01209 0.43052 3.42298
16 1V47 ADX 0.00006001 0.44223 3.4384
17 1O6B ADP 0.007678 0.4348 3.5503
18 1JZS MRC 0.00002254 0.52474 3.66748
19 2ZTG A5A 0.01124 0.4071 3.66748
20 2YN4 39J 0.02432 0.41352 3.81356
21 1QB7 ADE 0.02538 0.40411 3.81356
22 1JPA ANP 0.01162 0.43753 3.84615
23 4MAF ADX 0.0001409 0.49415 3.9604
24 3C8Z 5CA 0.0000004914 0.5921 4.15648
25 3L8G GMB 0.03709 0.40329 4.27807
26 1MFI FHC 0.02987 0.40742 4.38596
27 1H3F TYE 0.007502 0.43803 4.40098
28 1Y42 TYR 0.0192 0.41854 4.59184
29 2GKS ADP 0.0003985 0.46027 4.64548
30 4C2C ALA ALA ALA 0.04135 0.40009 4.64548
31 4A91 GLU 0.008088 0.42812 4.69799
32 2X1L ADN 0.0000009078 0.60968 4.88998
33 3R4S SLB 0.003799 0.45154 4.88998
34 3COW 52H 0.000005874 0.43172 4.88998
35 2RBK VN4 0.003847 0.45327 4.98084
36 2PID YSA 0.000000278 0.56538 5.05618
37 2H29 DND 0.0002159 0.43106 5.29101
38 3V0H I3P 0.0414 0.40072 5.30973
39 4ME6 ADP 0.03032 0.41043 5.37897
40 3EF0 ALF 0.03301 0.40557 5.62347
41 3HAV ATP 0.01905 0.42027 5.68562
42 3QX9 ATP 0.009467 0.4367 5.7971
43 3KFL ME8 0.0000004671 0.56206 5.86797
44 1KQN NAD 0.005062 0.40102 6.09319
45 1PFY MSP 0.0000009139 0.55592 6.11247
46 1N1D C2G 0.0007873 0.43663 6.20155
47 2QTR NXX 0.00006137 0.44044 6.34921
48 2CBZ ATP 0.0289 0.41519 6.60147
49 3T4L ZEA 0.01455 0.40194 7.09046
50 2OUA AES 0.0178 0.41395 7.97872
51 1Q11 TYE 0.002535 0.465 8.33333
52 3H0L ADP 0.02681 0.40674 8.51064
53 3FAL REA 0.01781 0.4045 8.67769
54 1YQC GLV 0.03907 0.41237 8.82353
55 5LLT DND 0.00032 0.42852 8.92019
56 4TS1 TYR 0.007139 0.44129 9.09091
57 1JIL 485 0.00001003 0.53464 9.29095
58 1X8X TYR 0.005396 0.43798 9.31677
59 1K4M NAD 0.0001947 0.45383 9.38967
60 3AFH GSU 0.000001177 0.58915 10.2689
61 5TH5 MET 0.04175 0.40059 10.6464
62 1F9A ATP 0.003004 0.42596 12.5
63 1M5W DXP 0.04136 0.40075 14.4033
64 1L5Y BEF 0.002113 0.46159 14.8387
65 2J5B TYE 0.008762 0.42908 14.9425
66 1ZX5 LFR 0.02642 0.41696 15.6667
67 2JEN GLC GLC XYS XYS 0.02121 0.41201 15.7088
68 1L7P SEP 0.007333 0.43583 16.1137
69 1GZF NIR 0.0409 0.40101 16.5877
70 5V49 8WA 0.0001229 0.46597 18.0929
71 2CYC TYR 0.006803 0.44364 18.4
72 3LQV ADE 0.008682 0.43258 25.641
73 2CYB TYR 0.02374 0.40965 32.1981
Pocket No.: 2; Query (leader) PDB : 4J75; Ligand: TYM; 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: 4j75.bio1) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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