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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;
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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 (17)
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 5N5U - AMP C10 H14 N5 O7 P c1nc(c2c(n....
10 2HGZ - PBF C16 H15 N O3 c1ccc(cc1)....
11 4PBR - 2L7 C13 H17 Br N2 O3 CC(C)(C(=O....
12 5L7P - BUU C16 H16 N2 O6 c1ccc(c(c1....
13 2PXH - BP5 C13 H13 N3 O2 c1ccnc(c1)....
14 3N2Y - TEF C10 H11 N5 O2 c1cc(ccc1C....
15 1ZH6 - 4AF C11 H13 N O3 CC(=O)c1cc....
16 4PBS - 2L7 C13 H17 Br N2 O3 CC(C)(C(=O....
17 1ZH0 - NAL C13 H13 N O2 c1ccc2cc(c....
50% Homology Family (22)
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 5N5U - AMP C10 H14 N5 O7 P c1nc(c2c(n....
10 2HGZ - PBF C16 H15 N O3 c1ccc(cc1)....
11 4PBR - 2L7 C13 H17 Br N2 O3 CC(C)(C(=O....
12 5L7P - BUU C16 H16 N2 O6 c1ccc(c(c1....
13 2PXH - BP5 C13 H13 N3 O2 c1ccnc(c1)....
14 3N2Y - TEF C10 H11 N5 O2 c1cc(ccc1C....
15 1ZH6 - 4AF C11 H13 N O3 CC(=O)c1cc....
16 4PBS - 2L7 C13 H17 Br N2 O3 CC(C)(C(=O....
17 1ZH0 - NAL C13 H13 N O2 c1ccc2cc(c....
18 2CYC - TYR C9 H11 N O3 c1cc(ccc1C....
19 1Q11 - TYE C9 H13 N O2 c1cc(ccc1C....
20 5THH - TYR C9 H11 N O3 c1cc(ccc1C....
21 3VGJ - YAP C19 H23 N6 O9 P c1cc(ccc1C....
22 2J5B - TYE C9 H13 N O2 c1cc(ccc1C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TYR; Similar ligands found: 30
No: Ligand ECFP6 Tc MDL keys Tc
1 TYR 1 1
2 DTY 1 1
3 TYC 0.694444 0.78125
4 PFF 0.657895 0.741935
5 4BF 0.615385 0.741935
6 PHI 0.615385 0.741935
7 TFQ 0.595238 0.666667
8 0A1 0.585366 0.9
9 7N8 0.585366 0.666667
10 4AF 0.585366 0.827586
11 4CF 0.571429 0.733333
12 PHE 0.564103 0.814815
13 DPN 0.564103 0.814815
14 34H 0.564103 0.666667
15 PBF 0.531915 0.8
16 PTR 0.521739 0.675
17 AEG 0.513514 0.689655
18 DAH 0.5 0.84375
19 3NF 0.478261 0.764706
20 TYE 0.475 0.8
21 IYR 0.468085 0.818182
22 YOF 0.468085 0.818182
23 4HP 0.447368 0.642857
24 2LT 0.444444 0.794118
25 485 0.442623 0.613636
26 E42 0.433962 0.9
27 33S 0.416667 0.741935
28 HPP 0.414634 0.655172
29 NAL 0.411765 0.766667
30 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 with APoc: 146
This union binding pocket(no: 1) in the query (biounit: 2cyb.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 4P5E N6P None
2 5D2H AKG 1.06007
3 2VBA P4T 1.23839
4 2A9D MTE 1.54799
5 2B96 ANN 1.62602
6 2C42 PYR 1.85759
7 2C42 TPP 1.85759
8 3IES M24 1.85759
9 2CJ9 SSA 1.85759
10 1F0X FAD 2.16718
11 4PYW ACE THR THR ALA ILE NH2 2.16718
12 2BII MTV 2.16718
13 4XDA RIB 2.26537
14 3TAY MN0 2.45399
15 3ILR IXD 2.47678
16 3ILR SGN 2.47678
17 3TWO NDP 2.47678
18 1EQ2 NAP 2.58065
19 1H65 GDP 2.59259
20 6GW4 CHO 2.60586
21 3ZF8 GDP 2.62295
22 3C9U ADP 2.78638
23 3C9U TPP 2.78638
24 2X6T NAP 2.78638
25 2J3M PRI 2.78638
26 2J3M ATP 2.78638
27 5W19 9TD 2.78638
28 1GZF ADP 2.8436
29 4RHE FMN 2.87081
30 1O6B ADP 2.95858
31 3COW 52H 2.99003
32 4A91 GLU 3.02013
33 2V0C LEU LMS 3.09598
34 1EU1 MGD 3.09598
35 4YNU FAD 3.09598
36 6C6O ENG 3.09598
37 2PT9 2MH 3.11526
38 2PT9 S4M 3.11526
39 4WUJ FMN 3.40136
40 2IU8 PLM 3.40557
41 2XCG XCG 3.40557
42 2YNE NHW 3.40557
43 2YNE YNE 3.40557
44 1SOX MTE 3.40557
45 5MRH Q9Z 3.40557
46 5WA0 MSS 3.40557
47 6MPT C30 3.4965
48 3ND6 ATP 3.50877
49 3LF0 ATP 3.50877
50 4QAC KK3 3.68664
51 5LRT ADP 3.71517
52 4Z87 GDP 3.71517
53 2IV2 2MD 3.71517
54 5XIJ ANP 3.71517
55 5XIJ 873 3.71517
56 3NEM AMO 3.71517
57 3P7N FMN 3.87597
58 3VZS NAP 3.89105
59 1F5F DHT 3.90244
60 4TW7 37K 3.90625
61 4Q5M ROC 3.94089
62 4OIV XX9 3.9823
63 5MM0 GDD 4.02477
64 4KVL PLM 4.02477
65 4FXQ G9L 4.02477
66 5O0B 9FE 4.32099
67 1DMR PGD 4.33437
68 1J09 GLU 4.33437
69 5OC1 FAD 4.33437
70 3C8Z 5CA 4.33437
71 5XIO HFG 4.33437
72 2O3Z AI7 4.42804
73 1KDK DHT 4.51977
74 2NNQ T4B 4.58015
75 1YQS BSA 4.64396
76 2RKV COA 4.64396
77 1LSH PLD 4.64396
78 2GUE NAG 4.91803
79 5DJU FMN 4.91803
80 3GZ8 APR 4.93827
81 6GG9 FMN 4.93827
82 1G0N NDP 4.947
83 3GPO APR 4.95356
84 2JDR GLY ARG PRO ARG THR THR SER PHE ALA GLU 4.95356
85 2JDR L20 4.95356
86 3KFL ME8 4.95356
87 4NAT 2W5 5
88 4NAT ADP 5
89 3NZK C90 5.14469
90 3C6K SPD 5.26316
91 3C6K MTA 5.26316
92 6D6L FY4 5.29412
93 2PR5 FMN 5.30303
94 2V0U FMN 5.47945
95 2V92 ATP 5.73248
96 2V92 AMP 5.73248
97 3A5Z KAA 5.75916
98 3DJF BC3 5.92335
99 1SIV PSI 6.06061
100 1VA6 P2S 6.19195
101 1VA6 ADP 6.19195
102 1QPB PYM 6.19195
103 1QPB TPP 6.19195
104 4NG2 OHN 6.19469
105 6FA4 D1W 6.35838
106 3LVW GSH 6.50155
107 2WKQ FMN 6.50155
108 2VZZ SCA 6.88073
109 5G3N X28 7.08661
110 5U3B 7TD 7.35786
111 2VBF TPP 7.43034
112 2NYA MGD 7.43034
113 3P3G 3P3 7.66667
114 3P3G UKW 7.66667
115 5V49 MET 7.73994
116 5V49 8WA 7.73994
117 4XSH NAI 7.82123
118 3R96 AMP 7.97872
119 3R96 ACO 7.97872
120 2GJ5 VD3 8.02469
121 4EN4 GT1 8.33333
122 4EN4 ATP 8.33333
123 4EN4 GT0 8.33333
124 4LGY ADP 8.35913
125 2XTS MTE 8.97833
126 1GEE NAD 9.1954
127 1JNR FAD 9.59752
128 4HIA FMN 9.65909
129 4HA6 FAD 9.90712
130 5UKL SIX 11.1455
131 5KY4 GDP 11.1455
132 5UXH GFB 11.4551
133 5KXQ GDP 12.3839
134 5KY5 GDP 12.5
135 5OCG 9R5 12.6984
136 2F5Z FAD 15.625
137 3UC5 ATP 17.8344
138 6BHV DQV 21.0332
139 2CM4 RCL 22.6667
140 3MWS 017 26.2626
141 5DK4 5BX 28.7926
142 5DK4 ATP 28.7926
143 4J75 TYM 32.1981
144 2G36 TRP 34.9845
145 2QIE 8CS 37.6623
146 1R6T TYM 40.2477
Pocket No.: 2; Query (leader) PDB : 2CYB; Ligand: TYR; Similar sites found with APoc: 35
This union binding pocket(no: 2) in the query (biounit: 2cyb.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 6E2B PT7 None
2 3T4L ZEA 1.48148
3 5KVS 6XR 1.54799
4 2JLD AG1 1.85759
5 5LYH 7B8 2.59067
6 1NAA 6FA 3.09598
7 4YNU LGC 3.09598
8 4WNK 453 3.09598
9 1HDC CBO 3.14961
10 4XTX 590 3.33333
11 2I7N ACO 3.33333
12 5TH5 7C5 3.40557
13 3CL7 HYN 3.57143
14 1F8G NAD 3.71517
15 2VK4 TPP 4.33437
16 3ACL 3F1 4.39189
17 1ZB6 GST 4.56026
18 4Q0P 0MK 4.61538
19 2RKV ZBA 4.64396
20 4I4Z 2NE 4.72727
21 2Z6D FMN 6.15385
22 1WUR 8DG 6.36364
23 5A3T MMK 6.81115
24 2ADA HPR 7.38636
25 4BVA T3 7.43034
26 5LHT TIH 7.48299
27 1N9L FMN 8.25688
28 5KF6 FAD 8.66873
29 5KF6 TFB 8.66873
30 3QX9 ATP 8.69565
31 5ANU 58T 9.49367
32 5MZY 8EZ 9.67742
33 1USF NAP 14.0449
34 1USF FMN 14.0449
35 3RMK BML 20.4819
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