Receptor
PDB id Resolution Class Description Source Keywords
2PID 2.2 Å EC: 6.1.1.1 CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL TYROSYL-TRNA SYNTHE COMPLEX WITH AN ADENYLATE ANALOG HOMO SAPIENS AMINOACYL-TRNA SYNTHETASE PROTEIN-SUBSTRATE COMPLEX ATP-BILIGASE MITOCHONDRION NUCLEOTIDE-BINDING PROTEIN BIOSYNTH
Ref.: CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL TYROSYL-TR SYNTHETASE REVEALS COMMON AND IDIOSYNCRATIC FEATURE STRUCTURE V. 15 1505 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
YSA A:384;
B:384;
Valid;
Valid;
none;
none;
submit data
509.493 C19 H23 N7 O8 S c1cc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2PID 2.2 Å EC: 6.1.1.1 CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL TYROSYL-TRNA SYNTHE COMPLEX WITH AN ADENYLATE ANALOG HOMO SAPIENS AMINOACYL-TRNA SYNTHETASE PROTEIN-SUBSTRATE COMPLEX ATP-BILIGASE MITOCHONDRION NUCLEOTIDE-BINDING PROTEIN BIOSYNTH
Ref.: CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL TYROSYL-TR SYNTHETASE REVEALS COMMON AND IDIOSYNCRATIC FEATURE STRUCTURE V. 15 1505 2007
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 12 families.
1 2PID - YSA C19 H23 N7 O8 S c1cc(ccc1C....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 2PID - YSA C19 H23 N7 O8 S c1cc(ccc1C....
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1WQ4 - TYR C9 H11 N O3 c1cc(ccc1C....
2 2YXN - AZY C9 H10 N4 O3 c1cc(c(cc1....
3 1WQ3 - IYR C9 H10 I N O3 c1cc(c(cc1....
4 1X8X - TYR C9 H11 N O3 c1cc(ccc1C....
5 1Y42 - TYR C9 H11 N O3 c1cc(ccc1C....
6 1JIL ic50 = 4 nM 485 C17 H24 N2 O8 C[C@@H]1[C....
7 2PID - YSA C19 H23 N7 O8 S c1cc(ccc1C....
8 1TYB - TYR C9 H11 N O3 c1cc(ccc1C....
9 4TS1 Kd = 11.6 uM TYR C9 H11 N O3 c1cc(ccc1C....
10 1TYD - TYR C9 H11 N O3 c1cc(ccc1C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: YSA; Similar ligands found: 204
No: Ligand ECFP6 Tc MDL keys Tc
1 YSA 1 1
2 SSA 0.76087 0.952941
3 5CA 0.744681 0.952941
4 A5A 0.731183 0.940476
5 LSS 0.729167 0.931035
6 DSZ 0.729167 0.952941
7 GSU 0.72449 0.952941
8 KAA 0.707071 0.920455
9 WSA 0.700935 0.987952
10 VMS 0.697917 0.918605
11 54H 0.697917 0.918605
12 53H 0.690722 0.908046
13 TSB 0.690722 0.929412
14 52H 0.680412 0.908046
15 NSS 0.66 0.952941
16 NVA LMS 0.653465 0.909091
17 LEU LMS 0.647059 0.909091
18 G5A 0.645833 0.952941
19 YAP 0.632075 0.847059
20 D3Y 0.607843 0.752941
21 5AS 0.6 0.886364
22 P5A 0.579439 0.910112
23 TYR AMP 0.567568 0.813953
24 4YB 0.561404 0.953488
25 649 0.555556 0.954023
26 AHX 0.53211 0.806818
27 FA5 0.530973 0.835294
28 SON 0.53 0.793103
29 CA0 0.524752 0.781609
30 SLU 0.52381 0.94186
31 5AL 0.52381 0.790698
32 3NZ 0.522523 0.747126
33 AMP 0.520833 0.776471
34 A 0.520833 0.776471
35 5X8 0.519608 0.729412
36 SRP 0.514019 0.813953
37 AMP MG 0.510204 0.738636
38 ABM 0.50505 0.758621
39 A2D 0.50505 0.8
40 DLL 0.504505 0.811765
41 FYA 0.504425 0.811765
42 AN2 0.5 0.790698
43 SRA 0.5 0.802326
44 XAH 0.5 0.78022
45 AMO 0.495495 0.813953
46 ADX 0.495146 0.894118
47 AU1 0.495146 0.781609
48 A12 0.49505 0.772727
49 AP2 0.49505 0.772727
50 BA3 0.49505 0.8
51 AOC 0.494949 0.697674
52 NB8 0.491228 0.806818
53 B4P 0.490196 0.8
54 AP5 0.490196 0.8
55 ADP 0.490196 0.77907
56 5CD 0.48913 0.682353
57 7MD 0.487395 0.78022
58 8QN 0.486486 0.790698
59 GAP 0.485981 0.761364
60 WAQ 0.482456 0.775281
61 LAD 0.482456 0.777778
62 M33 0.480769 0.770115
63 ADP MG 0.480769 0.75
64 TXA 0.478261 0.772727
65 5N5 0.478261 0.674419
66 ME8 0.478261 0.78022
67 DAL AMP 0.477477 0.770115
68 MAP 0.477477 0.764045
69 SAH 0.476636 0.712644
70 SFG 0.47619 0.697674
71 ACP 0.47619 0.781609
72 ADP BEF 0.47619 0.733333
73 ATP 0.47619 0.77907
74 50T 0.47619 0.75
75 BEF ADP 0.47619 0.733333
76 3UK 0.473684 0.802326
77 OOB 0.473214 0.811765
78 XYA 0.472527 0.694118
79 RAB 0.472527 0.694118
80 ADN 0.472527 0.694118
81 ANP 0.472222 0.781609
82 APC 0.471698 0.772727
83 AQP 0.471698 0.77907
84 5FA 0.471698 0.77907
85 APR 0.471698 0.77907
86 AR6 0.471698 0.77907
87 PRX 0.471698 0.741573
88 9SN 0.470085 0.766667
89 3DH 0.469388 0.678161
90 PAJ 0.469027 0.73913
91 4AD 0.469027 0.804598
92 TYM 0.467742 0.835294
93 AD9 0.46729 0.761364
94 AGS 0.46729 0.804598
95 SAP 0.46729 0.804598
96 RBY 0.46729 0.772727
97 SA8 0.46729 0.663043
98 ADP PO3 0.46729 0.776471
99 ADV 0.46729 0.772727
100 1ZZ 0.465517 0.723404
101 00A 0.464912 0.775281
102 7MC 0.464 0.763441
103 ATP MG 0.462963 0.75
104 ANP MG 0.459459 0.764045
105 SMM 0.459459 0.680851
106 S7M 0.459459 0.684783
107 TAT 0.458716 0.793103
108 ACQ 0.458716 0.781609
109 SAM 0.458716 0.684783
110 AMP DBH 0.458333 0.761364
111 A4D 0.457447 0.694118
112 A3S 0.457143 0.729412
113 ADQ 0.45614 0.781609
114 6RE 0.455446 0.67033
115 M2T 0.453608 0.666667
116 DTA 0.453608 0.729412
117 PTJ 0.452991 0.747253
118 YLC 0.452381 0.76087
119 YLB 0.452381 0.744681
120 YLP 0.451613 0.744681
121 A22 0.451327 0.790698
122 ADP ALF 0.45045 0.725275
123 ATF 0.45045 0.752809
124 ALF ADP 0.45045 0.725275
125 SAI 0.449541 0.685393
126 MYR AMP 0.449153 0.705263
127 KB1 0.449153 0.673913
128 ADP BMA 0.448276 0.761364
129 OAD 0.448276 0.781609
130 25A 0.447368 0.8
131 A3N 0.446602 0.651685
132 J7C 0.446602 0.677778
133 ADP VO4 0.446429 0.770115
134 VO4 ADP 0.446429 0.770115
135 PR8 0.444444 0.769231
136 ARG AMP 0.443548 0.734043
137 LAQ 0.443548 0.76087
138 0UM 0.443478 0.655914
139 A1R 0.443478 0.775281
140 EP4 0.443299 0.644444
141 EEM 0.441441 0.648936
142 3OD 0.440678 0.781609
143 48N 0.44 0.766667
144 4UU 0.439024 0.784091
145 DND 0.436508 0.793103
146 NXX 0.436508 0.793103
147 A3T 0.435185 0.697674
148 5SV 0.434783 0.709677
149 MTA 0.434343 0.678161
150 IOT 0.434109 0.736842
151 A A 0.432203 0.77907
152 7C5 0.430894 0.719101
153 YLA 0.430769 0.744681
154 A7D 0.429907 0.701149
155 LPA AMP 0.428571 0.741935
156 GJV 0.428571 0.663043
157 S4M 0.428571 0.645833
158 JB6 0.428571 0.816092
159 BIS 0.428571 0.736264
160 AYB 0.427481 0.736842
161 NAX 0.425197 0.788889
162 25L 0.425 0.790698
163 NAD IBO 0.424242 0.764045
164 TAD 0.424 0.777778
165 K15 0.423729 0.642105
166 VRT 0.423423 0.696629
167 A3G 0.423077 0.72093
168 DSH 0.423077 0.677778
169 4UV 0.422764 0.784091
170 TXE 0.421875 0.775281
171 OMR 0.421875 0.715789
172 LA8 ALF 3PG 0.421875 0.73913
173 ALF ADP 3PG 0.421875 0.73913
174 COD 0.421053 0.739583
175 ATP A A A 0.418033 0.788235
176 ZAS 0.417476 0.693182
177 67D 0.416667 0.931035
178 SXZ 0.416667 0.684783
179 YLY 0.416058 0.736842
180 62X 0.415254 0.628866
181 A5D 0.414414 0.729412
182 TXD 0.414062 0.775281
183 6V0 0.414062 0.766667
184 NAI 0.414062 0.775281
185 MHZ 0.412844 0.65625
186 MAO 0.411215 0.709677
187 A3P 0.411215 0.776471
188 AF3 ADP 3PG 0.410853 0.73913
189 NAD 0.410448 0.811765
190 GEK 0.410256 0.727273
191 NEC 0.409524 0.636364
192 AHZ 0.409449 0.723404
193 2VA 0.409091 0.681818
194 3AM 0.407767 0.744186
195 BT5 0.407407 0.755319
196 CNA 0.406015 0.813953
197 AFH 0.404762 0.758242
198 AR6 AR6 0.404762 0.77907
199 A3D 0.404412 0.802326
200 5AD 0.404255 0.630952
201 4UW 0.403101 0.758242
202 7D5 0.401961 0.707865
203 GTA 0.401575 0.741935
204 NAQ 0.4 0.766667
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2PID; Ligand: YSA; Similar sites found: 68
This union binding pocket(no: 1) in the query (biounit: 2pid.bio1) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3KFL ME8 0.0001443 0.45377 1.1236
2 3ZIU LSS 0.00003857 0.46675 1.96629
3 5IRN ADP 0.01717 0.40053 1.96629
4 2XZ9 PYR 0.008463 0.43715 2.16049
5 5FJJ MAN 0.002738 0.45201 2.24719
6 1J09 GLU 0.0004181 0.41774 2.24719
7 3COW 52H 0.00001517 0.41256 2.24719
8 4AUT FAD 0.007318 0.40386 2.24719
9 1J09 ATP 0.001222 0.40136 2.24719
10 1KQN NAD 0.001865 0.42094 2.50896
11 3UC5 ATP 0.01443 0.40408 2.54777
12 3LQV ADE 0.004604 0.4495 2.6087
13 1M2Z BOG 0.01037 0.41783 2.72374
14 2X3F APC 0.0000337 0.48369 2.80899
15 2B6N ALA PRO THR 0.02706 0.41166 2.8777
16 3ROE THM 0.02706 0.40524 3.01887
17 5E5U MLI 0.01763 0.41643 3.0303
18 3VSV XYS 0.03343 0.40773 3.08989
19 5DZT AMP 0.03499 0.40553 3.08989
20 3BER AMP 0.022 0.40596 3.21285
21 5LLT DND 0.0003712 0.42312 3.28639
22 4A91 GLU 0.004271 0.43537 3.3557
23 2V0C LEU LMS 0.00005111 0.4633 3.37079
24 4F8L AES 0.03131 0.41754 3.44828
25 5V49 8WA 0.0004383 0.41156 3.65169
26 2VOH CIT 0.002708 0.4054 3.82166
27 4XH0 ADP 0.0218 0.41614 3.93258
28 1XQD DND 0.008116 0.4122 3.93258
29 1PFY MSP 0.000005824 0.50201 3.99274
30 2X1L ADN 0.00001227 0.55372 4.21348
31 2H29 DND 0.00004452 0.48577 4.2328
32 1V47 ADX 0.001095 0.40208 4.58453
33 2XG5 EC5 0.02401 0.40012 4.62428
34 2XG5 EC2 0.02401 0.40012 4.62428
35 1N1D C2G 0.0004075 0.4466 4.65116
36 4PQG NAG 0.03103 0.40215 4.77528
37 4L80 OXL 0.02134 0.40762 4.88506
38 5T52 A2G 0.02939 0.40338 4.95868
39 4NAT 2W5 0.001285 0.43367 5
40 4NAT ADP 0.006231 0.43367 5
41 3BD9 A3P 0.02142 0.40283 5
42 4J75 TYM 0.000000278 0.56538 5.05618
43 3I7V B4P 0.005428 0.40467 5.22388
44 2Z8L NAG FUC SIA GAL 0.04021 0.40009 5.28846
45 1RL4 BRR 0.02037 0.41161 5.31915
46 4C2C ALA ALA ALA 0.006284 0.44721 5.33708
47 2GKS ADP 0.002092 0.42776 5.61798
48 2ZE3 AKG 0.02155 0.41593 5.81818
49 1RVV INI 0.02981 0.40306 5.84416
50 1GQ2 OXL 0.01933 0.41929 5.89888
51 4F9U PBD 0.03697 0.40211 6.08974
52 3UEC ALA ARG TPO LYS 0.02017 0.41874 6.16438
53 2GMP NAG MAN 0.04119 0.40367 6.46067
54 1P7T PYR 0.01462 0.40338 6.74157
55 3SJK LYS PRO VAL LEU ARG THR ALA 0.01887 0.4193 6.84211
56 1R6T TYM 0.0000006229 0.48963 7.54717
57 1R1Q ACE ARG GLU PTR VAL ASN VAL 0.04176 0.402 8
58 1R6U TYM 0.00000184 0.52197 8.23799
59 1O9U ADZ 0.01597 0.43321 8.28571
60 2QTR NXX 0.00001139 0.46054 8.46561
61 1XVB BBU 0.02672 0.40426 8.98876
62 1KC7 PPR 0.0055 0.45079 9.83146
63 3C8Z 5CA 0.0000001746 0.60949 10.1124
64 3AFH GSU 0.00001656 0.45436 10.3933
65 1K4M NAD 0.00002296 0.48832 10.6742
66 5HBN RPI 0.022 0.40989 11.5385
67 1JZS MRC 0.00006725 0.4418 13.2022
68 3HL4 CDC 0.002538 0.42768 13.5593
Pocket No.: 2; Query (leader) PDB : 2PID; Ligand: YSA; 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: 2pid.bio1) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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