Receptor
PDB id Resolution Class Description Source Keywords
2CYB 1.8 Å EC: 6.1.1.1 CRYSTAL STRUCTURE OF TYROSYL-TRNA SYNTHETASE COMPLEXED WITH L-TYROSINE FROM ARCHAEOGLOBUS FULGIDUS ARCHAEOGLOBUS FULGIDUS ROSSMANN-FOLD STRUCTURAL GENOMICS NPPSFA NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI LIGASE
Ref.: CRYSTAL STRUCTURES OF TYROSYL-TRNA SYNTHETASES FROM ARCHAEA J.MOL.BIOL. V. 355 395 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
TYR B:401;
B:501;
Valid;
Valid;
none;
none;
submit data
181.189 C9 H11 N O3 c1cc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2CYB 1.8 Å EC: 6.1.1.1 CRYSTAL STRUCTURE OF TYROSYL-TRNA SYNTHETASE COMPLEXED WITH L-TYROSINE FROM ARCHAEOGLOBUS FULGIDUS ARCHAEOGLOBUS FULGIDUS ROSSMANN-FOLD STRUCTURAL GENOMICS NPPSFA NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI LIGASE
Ref.: CRYSTAL STRUCTURES OF TYROSYL-TRNA SYNTHETASES FROM ARCHAEA J.MOL.BIOL. V. 355 395 2006
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 12 families.
1 2CYB - TYR C9 H11 N O3 c1cc(ccc1C....
70% Homology Family (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 2CYB - TYR C9 H11 N O3 c1cc(ccc1C....
2 4NX2 - 2LT C9 H9 Cl2 N O3 c1c(cc(c(c....
3 3QE4 - 4CF C10 H10 N2 O2 c1cc(ccc1C....
4 4NDA - NIY C9 H10 N2 O5 c1cc(c(cc1....
5 3D6V - TFQ C11 H12 F3 N O2 c1cc(ccc1C....
6 2AG6 - 4BF C9 H10 Br N O2 c1cc(ccc1C....
7 3D6U - T11 C11 H12 F3 N3 O2 c1cc(ccc1C....
8 4PBT - 2LQ C18 H24 N2 O3 c1cc(ccc1C....
9 2HGZ - PBF C16 H15 N O3 c1ccc(cc1)....
10 4PBR - 2L7 C13 H17 Br N2 O3 CC(C)(C(=O....
11 5L7P - BUU C16 H16 N2 O6 c1ccc(c(c1....
12 2PXH - BP5 C13 H13 N3 O2 c1ccnc(c1)....
13 3N2Y - TEF C10 H11 N5 O2 c1cc(ccc1C....
14 1ZH6 - 4AF C11 H13 N O3 CC(=O)c1cc....
15 4PBS - 2L7 C13 H17 Br N2 O3 CC(C)(C(=O....
16 1ZH0 - NAL C13 H13 N O2 c1ccc2cc(c....
50% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2CYB - TYR C9 H11 N O3 c1cc(ccc1C....
2 4NX2 - 2LT C9 H9 Cl2 N O3 c1c(cc(c(c....
3 3QE4 - 4CF C10 H10 N2 O2 c1cc(ccc1C....
4 4NDA - NIY C9 H10 N2 O5 c1cc(c(cc1....
5 3D6V - TFQ C11 H12 F3 N O2 c1cc(ccc1C....
6 2AG6 - 4BF C9 H10 Br N O2 c1cc(ccc1C....
7 3D6U - T11 C11 H12 F3 N3 O2 c1cc(ccc1C....
8 4PBT - 2LQ C18 H24 N2 O3 c1cc(ccc1C....
9 2HGZ - PBF C16 H15 N O3 c1ccc(cc1)....
10 4PBR - 2L7 C13 H17 Br N2 O3 CC(C)(C(=O....
11 5L7P - BUU C16 H16 N2 O6 c1ccc(c(c1....
12 2PXH - BP5 C13 H13 N3 O2 c1ccnc(c1)....
13 3N2Y - TEF C10 H11 N5 O2 c1cc(ccc1C....
14 1ZH6 - 4AF C11 H13 N O3 CC(=O)c1cc....
15 4PBS - 2L7 C13 H17 Br N2 O3 CC(C)(C(=O....
16 1ZH0 - NAL C13 H13 N O2 c1ccc2cc(c....
17 2CYC - TYR C9 H11 N O3 c1cc(ccc1C....
18 1Q11 - TYE C9 H13 N O2 c1cc(ccc1C....
19 5THH - TYR C9 H11 N O3 c1cc(ccc1C....
20 3VGJ - YAP C19 H23 N6 O9 P c1cc(ccc1C....
21 2J5B - TYE C9 H13 N O2 c1cc(ccc1C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TYR; Similar ligands found: 28
No: Ligand ECFP6 Tc MDL keys Tc
1 DTY 1 1
2 TYR 1 1
3 TYC 0.694444 0.78125
4 PFF 0.657895 0.741935
5 PHI 0.615385 0.741935
6 4BF 0.615385 0.741935
7 TFQ 0.595238 0.666667
8 0A1 0.585366 0.9
9 4AF 0.585366 0.827586
10 4CF 0.571429 0.733333
11 DPN 0.564103 0.814815
12 PHE 0.564103 0.814815
13 34H 0.564103 0.666667
14 PBF 0.531915 0.8
15 PTR 0.521739 0.675
16 AEG 0.513514 0.689655
17 DAH 0.5 0.84375
18 3NF 0.478261 0.764706
19 TYE 0.475 0.8
20 IYR 0.468085 0.818182
21 4HP 0.447368 0.642857
22 2LT 0.444444 0.794118
23 485 0.442623 0.613636
24 E42 0.433962 0.9
25 33S 0.416667 0.741935
26 HPP 0.414634 0.655172
27 NAL 0.411765 0.766667
28 AZY 0.4 0.658537
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2CYB; Ligand: TYR; Similar sites found: 106
This union binding pocket(no: 1) in the query (biounit: 2cyb.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5D2H AKG 0.0141 0.40883 1.06007
2 2VBA P4T 0.03382 0.40109 1.23839
3 2A9D MTE 0.02988 0.40336 1.54799
4 2C42 PYR 0.01832 0.42271 1.85759
5 2C42 TPP 0.01832 0.42271 1.85759
6 3IES M24 0.04452 0.40549 1.85759
7 1F0X FAD 0.02066 0.43059 2.16718
8 4PYW ACE THR THR ALA ILE NH2 0.02985 0.40569 2.16718
9 5W4W 9WG 0.04045 0.40538 2.16718
10 2BII MTV 0.03401 0.40003 2.16718
11 4XDA RIB 0.01596 0.40305 2.26537
12 3TAY MN0 0.03099 0.40429 2.45399
13 3ILR SGN 0.04352 0.41479 2.47678
14 3TWO NDP 0.02985 0.41296 2.47678
15 4CS4 ANP 0.02596 0.41924 2.55474
16 4CS4 AXZ 0.03206 0.41924 2.55474
17 1EQ2 NAP 0.006621 0.44718 2.58065
18 3ZF8 GDP 0.003902 0.43691 2.62295
19 3C9U ADP 0.008978 0.43141 2.78638
20 3C9U TPP 0.01933 0.42946 2.78638
21 2X6T NAP 0.01336 0.42736 2.78638
22 2J3M PRI 0.0157 0.42142 2.78638
23 2J3M ATP 0.01471 0.42111 2.78638
24 1GZF ADP 0.02086 0.40041 2.8436
25 1O6B ADP 0.003668 0.43151 2.95858
26 4A91 GLU 0.0006093 0.44376 3.02013
27 2V0C LEU LMS 0.01412 0.42429 3.09598
28 4YNU FAD 0.04507 0.41243 3.09598
29 2PT9 2MH 0.02332 0.41799 3.11526
30 2PT9 S4M 0.01567 0.41799 3.11526
31 2YNE NHW 0.04511 0.4279 3.40557
32 2YNE YNE 0.04511 0.4279 3.40557
33 4PW3 MSS 0.02344 0.40202 3.40557
34 1SOX MTE 0.03163 0.402 3.40557
35 5MRH Q9Z 0.01562 0.40184 3.40557
36 4DE9 VTP 0.0403 0.4062 3.4965
37 3ND6 ATP 0.01562 0.43172 3.50877
38 3LF0 ATP 0.03193 0.40033 3.50877
39 2I7C AAT 0.03747 0.40512 3.53357
40 3CL7 HYN 0.01051 0.40058 3.57143
41 4QAC KK3 0.03157 0.40265 3.68664
42 5LRT ADP 0.01016 0.43425 3.71517
43 2IV2 2MD 0.04214 0.40291 3.71517
44 3NEM AMO 0.03908 0.40075 3.71517
45 3P7N FMN 0.02289 0.40117 3.87597
46 3VZS NAP 0.03677 0.4175 3.89105
47 4TW7 37K 0.007523 0.4361 3.90625
48 4Q5M ROC 0.02339 0.41514 3.94089
49 4OIV XX9 0.0406 0.41078 3.9823
50 5LIA 6XN 0.02875 0.4334 4.02477
51 5MM0 GDD 0.02516 0.41119 4.02477
52 4FXQ G9L 0.01261 0.4027 4.02477
53 1DMR PGD 0.03005 0.43593 4.33437
54 2VK4 TPP 0.009257 0.43361 4.33437
55 1J09 GLU 0.01068 0.42407 4.33437
56 3C8Z 5CA 0.0207 0.40833 4.33437
57 2O3Z AI7 0.01538 0.45663 4.42804
58 2NNQ T4B 0.04287 0.41149 4.58015
59 1YQS BSA 0.04137 0.40765 4.64396
60 2RKV COA 0.04907 0.40232 4.64396
61 1LSH PLD 0.04972 0.40192 4.64396
62 5DJU FMN 0.01906 0.40894 4.91803
63 3GZ8 APR 0.01872 0.41034 4.93827
64 1G0N NDP 0.04815 0.41114 4.947
65 3GPO APR 0.0144 0.42125 4.95356
66 2JDR GLY ARG PRO ARG THR THR SER PHE ALA GLU 0.04847 0.41619 4.95356
67 2JDR L20 0.04847 0.41619 4.95356
68 3KFL ME8 0.02774 0.40477 4.95356
69 3NZK C90 0.01914 0.40688 5.14469
70 3IX8 TX3 0.001699 0.47474 5.20231
71 3A5Z KAA 0.02786 0.41245 5.75916
72 3DJF BC3 0.02457 0.40385 5.92335
73 1SIV PSI 0.02118 0.41878 6.06061
74 1QPB PYM 0.0352 0.40303 6.19195
75 1QPB TPP 0.0352 0.40303 6.19195
76 4NG2 OHN 0.001866 0.47175 6.19469
77 3LVW GSH 0.01942 0.43074 6.50155
78 5G3N X28 0.02964 0.40234 7.08661
79 5U3B 7TD 0.001152 0.48666 7.35786
80 3P3G UKW 0.002744 0.4636 7.66667
81 3P3G 3P3 0.002744 0.4636 7.66667
82 5V49 MET 0.008237 0.41123 7.73994
83 5V49 8WA 0.03878 0.40736 7.73994
84 4XSH NAI 0.03723 0.40119 7.82123
85 3R96 AMP 0.0208 0.42712 7.97872
86 3R96 ACO 0.0208 0.42712 7.97872
87 4RT1 C2E 0.01745 0.40842 8.03571
88 4LGY ADP 0.02573 0.4044 8.35913
89 2XTS MTE 0.02331 0.41132 8.97833
90 1O44 852 0.04333 0.4111 9.25926
91 4HIA FMN 0.005814 0.45591 9.65909
92 4HA6 FAD 0.0485 0.41012 9.90712
93 5UKL SIX 0.03104 0.40268 11.1455
94 5KY4 GDP 0.01722 0.4024 11.1455
95 5UXH GFB 0.01558 0.41125 11.4551
96 5KXQ GDP 0.0163 0.40382 12.3839
97 5KY5 GDP 0.01491 0.40661 12.5
98 2H29 DND 0.04161 0.40287 15.3439
99 2BLF MSS 0.02223 0.40577 16.0494
100 3UC5 ATP 0.01454 0.41375 17.8344
101 2CM4 RCL 0.001486 0.47374 22.6667
102 3MWS 017 0.02653 0.41271 26.2626
103 4J75 TYM 0.02374 0.40965 32.1981
104 2G36 TRP 0.000004023 0.57208 34.9845
105 2QIE 8CS 0.002237 0.45747 37.6623
106 1R6T TYM 0.01805 0.42686 40.2477
Pocket No.: 2; Query (leader) PDB : 2CYB; Ligand: TYR; 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: 2cyb.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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