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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: 217
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 DSZ 0.729167 0.952941
6 LSS 0.729167 0.931035
7 GSU 0.72449 0.952941
8 KAA 0.707071 0.920455
9 WSA 0.700935 0.987952
10 54H 0.697917 0.918605
11 VMS 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 0.920455
17 LEU LMS 0.647059 0.920455
18 G5A 0.645833 0.952941
19 YAP 0.632075 0.847059
20 8X1 0.607843 0.920455
21 D3Y 0.607843 0.752941
22 8PZ 0.601852 0.97619
23 5AS 0.6 0.886364
24 P5A 0.579439 0.910112
25 8Q2 0.577586 0.965116
26 LMS 0.569892 0.939759
27 TYR AMP 0.5625 0.825581
28 4YB 0.561404 0.953488
29 649 0.555556 0.954023
30 AHX 0.53211 0.806818
31 FA5 0.530973 0.835294
32 SON 0.53 0.793103
33 CA0 0.524752 0.781609
34 SLU 0.52381 0.94186
35 5AL 0.52381 0.790698
36 3NZ 0.522523 0.747126
37 A 0.520833 0.776471
38 AMP 0.520833 0.776471
39 5X8 0.519608 0.729412
40 SRP 0.514019 0.813953
41 ABM 0.50505 0.758621
42 A2D 0.50505 0.8
43 DLL 0.504505 0.811765
44 FYA 0.504425 0.811765
45 AN2 0.5 0.790698
46 XAH 0.5 0.78022
47 SRA 0.5 0.802326
48 AMO 0.495495 0.813953
49 ADX 0.495146 0.894118
50 AU1 0.495146 0.781609
51 A12 0.49505 0.772727
52 AP2 0.49505 0.772727
53 BA3 0.49505 0.8
54 AOC 0.494949 0.697674
55 NB8 0.491228 0.806818
56 B4P 0.490196 0.8
57 ADP 0.490196 0.77907
58 AP5 0.490196 0.8
59 5CD 0.48913 0.682353
60 7MD 0.487395 0.78022
61 8QN 0.486486 0.790698
62 9ZA 0.486486 0.775281
63 9ZD 0.486486 0.775281
64 GAP 0.485981 0.761364
65 AT4 0.485437 0.793103
66 LAD 0.482456 0.777778
67 WAQ 0.482456 0.775281
68 M33 0.480769 0.770115
69 ME8 0.478261 0.78022
70 TXA 0.478261 0.772727
71 5N5 0.478261 0.674419
72 MAP 0.477477 0.764045
73 DAL AMP 0.477477 0.770115
74 SAH 0.476636 0.712644
75 50T 0.47619 0.75
76 ACP 0.47619 0.781609
77 ATP 0.47619 0.77907
78 SFG 0.47619 0.697674
79 HEJ 0.47619 0.77907
80 3UK 0.473684 0.802326
81 OOB 0.473214 0.811765
82 XYA 0.472527 0.694118
83 ADN 0.472527 0.694118
84 RAB 0.472527 0.694118
85 ANP 0.472222 0.781609
86 AQP 0.471698 0.77907
87 APR 0.471698 0.77907
88 APC 0.471698 0.772727
89 5FA 0.471698 0.77907
90 PRX 0.471698 0.741573
91 AR6 0.471698 0.77907
92 9SN 0.470085 0.766667
93 B5V 0.469565 0.813953
94 3DH 0.469388 0.678161
95 PAJ 0.469027 0.73913
96 4AD 0.469027 0.804598
97 TYM 0.467742 0.835294
98 ADV 0.46729 0.772727
99 SA8 0.46729 0.663043
100 AGS 0.46729 0.804598
101 ADP PO3 0.46729 0.776471
102 RBY 0.46729 0.772727
103 SAP 0.46729 0.804598
104 AD9 0.46729 0.761364
105 B5Y 0.466102 0.804598
106 9K8 0.465517 0.778947
107 1ZZ 0.465517 0.723404
108 00A 0.464912 0.775281
109 7MC 0.464 0.763441
110 SMM 0.459459 0.680851
111 S7M 0.459459 0.684783
112 ACQ 0.458716 0.781609
113 SAM 0.458716 0.684783
114 TAT 0.458716 0.793103
115 T99 0.458716 0.793103
116 AMP DBH 0.458333 0.761364
117 A4D 0.457447 0.694118
118 A3S 0.457143 0.729412
119 ADQ 0.45614 0.781609
120 6RE 0.455446 0.67033
121 B5M 0.453782 0.804598
122 DTA 0.453608 0.729412
123 M2T 0.453608 0.666667
124 PTJ 0.452991 0.747253
125 YLC 0.452381 0.76087
126 YLB 0.452381 0.744681
127 YLP 0.451613 0.744681
128 A22 0.451327 0.790698
129 ATF 0.45045 0.752809
130 ALF ADP 0.45045 0.725275
131 ADP ALF 0.45045 0.725275
132 SAI 0.449541 0.685393
133 MYR AMP 0.449153 0.705263
134 KB1 0.449153 0.673913
135 OAD 0.448276 0.781609
136 ADP BMA 0.448276 0.761364
137 25A 0.447368 0.8
138 A3N 0.446602 0.651685
139 J7C 0.446602 0.677778
140 6YZ 0.446429 0.781609
141 VO4 ADP 0.446429 0.770115
142 ADP VO4 0.446429 0.770115
143 PR8 0.444444 0.769231
144 LAQ 0.443548 0.76087
145 A1R 0.443478 0.775281
146 0UM 0.443478 0.655914
147 EP4 0.443299 0.644444
148 EEM 0.441441 0.648936
149 3OD 0.440678 0.781609
150 48N 0.44 0.766667
151 4UU 0.439024 0.784091
152 ARG AMP 0.439024 0.734043
153 NXX 0.436508 0.793103
154 DND 0.436508 0.793103
155 9X8 0.435897 0.784091
156 A3T 0.435185 0.697674
157 F2R 0.435115 0.744681
158 5SV 0.434783 0.709677
159 MTA 0.434343 0.678161
160 IOT 0.434109 0.736842
161 A A 0.432203 0.77907
162 A3R 0.431034 0.775281
163 7C5 0.430894 0.719101
164 YLA 0.430769 0.744681
165 A7D 0.429907 0.701149
166 JB6 0.428571 0.816092
167 S4M 0.428571 0.645833
168 BIS 0.428571 0.736264
169 GJV 0.428571 0.663043
170 LPA AMP 0.428571 0.741935
171 AYB 0.427481 0.736842
172 GA7 0.427419 0.772727
173 80F 0.425373 0.782609
174 NAX 0.425197 0.788889
175 25L 0.425 0.790698
176 DQV 0.424 0.811765
177 TAD 0.424 0.777778
178 K15 0.423729 0.642105
179 VRT 0.423423 0.696629
180 DSH 0.423077 0.677778
181 A3G 0.423077 0.72093
182 4UV 0.422764 0.784091
183 TXE 0.421875 0.775281
184 OMR 0.421875 0.715789
185 COD 0.421053 0.739583
186 ATP A A A 0.418033 0.788235
187 ZAS 0.417476 0.693182
188 67D 0.416667 0.931035
189 SXZ 0.416667 0.684783
190 YLY 0.416058 0.736842
191 62X 0.415254 0.628866
192 EO7 0.415094 0.896552
193 A5D 0.414414 0.729412
194 6V0 0.414062 0.766667
195 NAI 0.414062 0.775281
196 TXD 0.414062 0.775281
197 MHZ 0.412844 0.65625
198 MAO 0.411215 0.709677
199 A3P 0.411215 0.776471
200 AF3 ADP 3PG 0.410853 0.73913
201 AMP NAD 0.410448 0.790698
202 NAD 0.410448 0.811765
203 GEK 0.410256 0.727273
204 NEC 0.409524 0.636364
205 AHZ 0.409449 0.723404
206 2VA 0.409091 0.681818
207 3AM 0.407767 0.744186
208 BT5 0.407407 0.755319
209 CNA 0.406015 0.813953
210 AR6 AR6 0.404762 0.77907
211 AFH 0.404762 0.758242
212 A3D 0.404412 0.802326
213 5AD 0.404255 0.630952
214 4UW 0.403101 0.758242
215 7D5 0.401961 0.707865
216 GTA 0.401575 0.741935
217 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 with APoc: 165
This union binding pocket(no: 1) in the query (biounit: 2pid.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 3ZZQ TRP None
2 1SQL GUN None
3 3ZZS TRP None
4 3KFL ME8 1.1236
5 3ITA AIC 1.68539
6 6F5W KG1 1.68539
7 2ZPA ADP 1.68539
8 2V5K OXM 1.74216
9 2F59 INI 1.91083
10 4B5W PYR 1.95312
11 3ZIU LSS 1.96629
12 5C9P FUC 1.96629
13 2ZWS PLM 1.96629
14 5TSU CYS 1.96629
15 6BR9 6OU 1.96629
16 5IRN ADP 1.96629
17 4WBD CIT 1.96629
18 3HAV ATP 2.00669
19 5DK4 ATP 2.12766
20 5DK4 5BX 2.12766
21 2XZ9 PYR 2.16049
22 2VAR AMP 2.23642
23 1J09 GLU 2.24719
24 5FJJ MAN 2.24719
25 1J09 ATP 2.24719
26 1G51 AMP 2.24719
27 3COW 52H 2.24719
28 4AUT FAD 2.24719
29 2XOC ADP 2.29885
30 4FGC PQ0 2.42424
31 1XP8 AGS 2.45902
32 5VX9 FUC GAL NAG GAL BGC 2.48447
33 4PYA 2X3 2.48447
34 1KQN NAD 2.50896
35 6GNF GLC 2.52809
36 3UC5 ATP 2.54777
37 3LQV ADE 2.6087
38 3ZF8 GDP 2.62295
39 5NM7 GLY 2.63158
40 6B5K TYD 2.7027
41 1M2Z BOG 2.72374
42 1NXJ TLA 2.73224
43 6BR8 6OU 2.77778
44 2X3F APC 2.80899
45 5XQL C2E 2.80899
46 3IWJ NAD 2.80899
47 2B6N ALA PRO THR 2.8777
48 3ROE THM 3.01887
49 5E5U MLI 3.0303
50 3VSV XYS 3.08989
51 5DZT AMP 3.08989
52 1TUK PGM 3.08989
53 3BER AMP 3.21285
54 5A04 BGC 3.24484
55 5LLT DND 3.28639
56 4A91 GLU 3.3557
57 2V0C LEU LMS 3.37079
58 4LIK CIT 3.37079
59 4F8L AES 3.44828
60 6GR0 F8W 3.44828
61 3ND6 ATP 3.50877
62 4MAF ADX 3.65169
63 5V49 8WA 3.65169
64 1QHO MAL 3.65169
65 2VOH CIT 3.82166
66 4XH0 ADP 3.93258
67 4TVD BGC 3.93258
68 1XQD DND 3.93258
69 2CUN 3PG 3.93258
70 1PFY MSP 3.99274
71 1SBR VIB 4
72 4K55 H6P 4.03226
73 1TMX BEZ 4.09556
74 2X1L ADN 4.21348
75 2H29 DND 4.2328
76 4L9Z OXL 4.42478
77 2WD7 VGD 4.47761
78 3BP1 GUN 4.48276
79 6C0B MLI 4.48718
80 5Z5I XYP 4.49438
81 3UZO PLP 4.49438
82 1JT1 MCO 4.56274
83 1V47 ADX 4.58453
84 2XG5 EC5 4.62428
85 2XG5 EC2 4.62428
86 1N1D C2G 4.65116
87 5XET ME8 4.77528
88 1Q19 SSC 4.77528
89 6E1Q CFA 4.77528
90 4PQG NAG 4.77528
91 6MVU K4V 4.77528
92 5ZYN SIN 4.77528
93 4L80 OXL 4.88506
94 5GLN XYP XYP XYP 4.94186
95 5T52 A2G 4.95868
96 5X3D 7XL 5
97 4NAT 2W5 5
98 4NAT ADP 5
99 3BD9 A3P 5
100 4J75 TYM 5.05618
101 3W6G FLC 5.09259
102 1II7 DA 5.1051
103 1NE7 16G 5.19031
104 3I7V B4P 5.22388
105 2Z8L NAG FUC SIA GAL 5.28846
106 1RL4 BRR 5.31915
107 4C2C ALA ALA ALA 5.33708
108 5O0B 9FE 5.55556
109 6CHP F0Y 5.59006
110 2GKS ADP 5.61798
111 5Y0Q APC 5.61798
112 5Y0N ATP 5.61798
113 2ZE3 AKG 5.81818
114 1RVV INI 5.84416
115 1GQ2 OXL 5.89888
116 3RS8 ALA TRP LEU PHE GLU ALA 5.89888
117 5ZDK ATP 5.89888
118 4F9U PBD 6.08974
119 3UEC ALA ARG TPO LYS 6.16438
120 2VWT PYR 6.36704
121 1U0J ADP 6.46067
122 2GMP NAG MAN 6.46067
123 1JPA ANP 6.73077
124 3ICT ADP 6.74157
125 3ICS ADP 6.74157
126 1P7T PYR 6.74157
127 1YQT ADP 6.74157
128 3SJK LYS PRO VAL LEU ARG THR ALA 6.84211
129 5WXU FLC 7.02247
130 3QX9 ATP 7.24638
131 1R6T TYM 7.54717
132 3RK0 AMP 7.59494
133 1TL2 NDG 7.62712
134 1R1Q ACE ARG GLU PTR VAL ASN VAL 8
135 1R6U TYM 8.23799
136 1O9U ADZ 8.28571
137 1NLU IVA PHI TYB 8.42697
138 2QTR NXX 8.46561
139 3HRD NIO 8.75
140 1VKJ A3P 8.77193
141 1O6B ADP 8.87574
142 1F9A ATP 8.92857
143 1XVB BBU 8.98876
144 5O22 C3R 9.34256
145 1KC7 PPR 9.83146
146 1OJ4 ANP 9.89399
147 3C8Z 5CA 10.1124
148 3AFH GSU 10.3933
149 1WAP TRP 10.6667
150 1K4M NAD 10.6742
151 1YUM NCN 10.7438
152 2ZJ5 ADP 10.9551
153 5G6U TRP 11.1111
154 5Y0T TAT 11.236
155 1VBH PEP 11.7978
156 1JZS MRC 13.2022
157 3HL4 CDC 13.5593
158 5YV5 ADP 13.764
159 2QX0 PH2 14.4654
160 2W5P CL8 14.7651
161 3GUZ PAF 14.8876
162 3H0L ADP 14.8936
163 3ZIA ADP 15.873
164 3KIF GDL 16.9811
165 2G36 TRP 25.5618
Pocket No.: 2; Query (leader) PDB : 2PID; Ligand: YSA; Similar sites found with APoc: 34
This union binding pocket(no: 2) in the query (biounit: 2pid.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 1MID LAP None
2 1TZJ A3B 1.18343
3 5GWE GWM 1.40449
4 1IZC PYR 1.76991
5 2PEL LBT 2.11864
6 1F9V ADP 2.24719
7 1DNP MHF 2.24719
8 5VLQ ANP 2.80899
9 2RDG NDG FUC SIA GAL 3.06122
10 3BJU ATP 3.08989
11 3KIH GDL 3.09278
12 1NJJ GET 3.37079
13 2O2C G6Q 3.37079
14 4DDY DN6 4.18251
15 1XMV ADP 4.21348
16 5OPJ AHR 5.05618
17 3MKN DNB 5.06329
18 1XQP 8HG 5.46875
19 5HRA DAS 6.38298
20 2D3Y DU 6.39269
21 1Q8V MAN MAN MAN 6.46067
22 2PHR MAN MAN BMA MAN 6.46067
23 1GPM AMP 6.74157
24 3GD8 GOL 7.17489
25 6MJ7 ARG 7.27273
26 6BK3 UDP 7.30337
27 5CIC 51R 7.40741
28 3T0W DIW 8.13008
29 6GNO XDI 8.14815
30 4PTN PYR 8.98876
31 1YID ATP 9.68661
32 1W0O SIA 12.0787
33 3MBC NAP 16.0112
34 5N8V KZZ 18.8406
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