Receptor
PDB id Resolution Class Description Source Keywords
3NEL 1.95 Å EC: 6.1.1.12 ASPARTYL-TRNA SYNTHETASE COMPLEXED WITH ASPARTIC ACID THERMOCOCCUS KODAKARENSIS AMINOACYL-TRNA SYNTHETASE ROSSMANN FOLD OB FOLD AMINO ACIDTRNA LIGASE
Ref.: CRYSTAL STRUCTURE OF ASPARTYL-TRNA SYNTHETASE FROM PYROCOCCUS KODAKARAENSIS KOD: ARCHAEON SPECIFICITY CATALYTIC MECHANISM OF ADENYLATE FORMATION EMBO J. V. 17 5227 1998
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ASP A:500;
Valid;
none;
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133.103 C4 H7 N O4 C([C@...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3NEM 1.89 Å EC: 6.1.1.12 ASPARTYL-TRNA SYNTHETASE COMPLEXED WITH ASPARTYL ADENYLATE THERMOCOCCUS KODAKARENSIS ROSSMANN FOLD OB FOLD LIGASE
Ref.: CRYSTAL STRUCTURE OF ASPARTYL-TRNA SYNTHETASE FROM PYROCOCCUS KODAKARAENSIS KOD: ARCHAEON SPECIFICITY CATALYTIC MECHANISM OF ADENYLATE FORMATION EMBO J. V. 17 5227 1998
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1B8A - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
2 3NEL - ASP C4 H7 N O4 C([C@@H](C....
3 3NEM - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1B8A - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
2 3NEL - ASP C4 H7 N O4 C([C@@H](C....
3 3NEM - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 2XTI - NB8 C14 H20 N7 O10 P c1nc(c2c(n....
2 2XGT - NSS C14 H21 N8 O8 S c1nc(c2c(n....
3 1B8A - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 3NEL - ASP C4 H7 N O4 C([C@@H](C....
5 3NEM - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
6 1X54 - 4AD C14 H21 N7 O9 P c1nc(c2c(n....
7 1X55 - NSS C14 H21 N8 O8 S c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ASP; Similar ligands found: 32
No: Ligand ECFP6 Tc MDL keys Tc
1 ASP 1 1
2 DAS 1 1
3 ASN 0.636364 0.793103
4 SER 0.545455 0.714286
5 DBB 0.545455 0.692308
6 2RA 0.545455 0.689655
7 ABA 0.545455 0.692308
8 DSN 0.545455 0.714286
9 DCY 0.521739 0.703704
10 CYS 0.521739 0.703704
11 C2N 0.521739 0.666667
12 SD4 0.5 0.648649
13 DGL 0.481481 0.846154
14 GLU 0.481481 0.846154
15 GGL 0.481481 0.846154
16 DAB 0.48 0.612903
17 HSE 0.48 0.758621
18 LEU 0.461538 0.642857
19 AS2 0.461538 0.916667
20 HCS 0.461538 0.655172
21 CSO 0.461538 0.6875
22 NVA 0.461538 0.62069
23 API 0.461538 0.75
24 CSS 0.444444 0.633333
25 CSD 0.444444 0.615385
26 11C 0.433333 0.814815
27 UN1 0.433333 0.814815
28 GLN 0.428571 0.7
29 DGN 0.428571 0.7
30 NPI 0.40625 0.785714
31 NCD 0.4 0.705882
32 ONL 0.4 0.7
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3NEM; Ligand: ATP; Similar sites found: 62
This union binding pocket(no: 1) in the query (biounit: 3nem.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3KB6 NAD 0.02609 0.40351 1.49701
2 5UIU 8CG 0.01939 0.4113 1.54799
3 2ZTG A5A 0.0000000009736 0.64262 1.82648
4 2CJ9 SSA 0.0000004206 0.62279 1.82648
5 2CJA ATP 0.000001335 0.59247 1.82648
6 4DQ2 BTX 0.01624 0.41521 2.13415
7 1WLE SRP 0.0000005493 0.6172 2.28311
8 5VAD 91Y 0.0001511 0.52062 2.28311
9 3QO8 SSA 0.000006358 0.51099 2.28311
10 2JLB UDM 0.02179 0.4048 2.51142
11 4TSK NDP 0.01808 0.41025 2.57143
12 5TA6 79D 0.01038 0.42234 2.7933
13 3UH0 TSB 0.0001265 0.51215 2.96804
14 3E8N ATP 0.0285 0.41597 3.22581
15 3E8N VRA 0.0285 0.41597 3.22581
16 4IQY AR6 0.02331 0.40048 3.33333
17 3ERR AMP 0.0000165 0.53434 3.42466
18 3CV2 COA 0.00885 0.42096 3.42466
19 1Q19 APC 0.007969 0.42026 3.42466
20 3MVH WFE 0.01359 0.41913 3.50877
21 5N87 N66 0.03152 0.40616 3.51438
22 1SES AMP 0.000002638 0.57695 3.56295
23 1SES AHX 0.000004262 0.51785 3.56295
24 2Y88 2ER 0.03838 0.40272 3.68852
25 4XDZ NDP 0.02614 0.40084 3.79009
26 4H2W AMP 0.0000005608 0.55447 3.8835
27 4H2X G5A 0.000001211 0.51828 3.8835
28 4H2W 5GP 0.000007255 0.49907 3.8835
29 3MF2 AMP 0.000001204 0.60903 4.33526
30 3TEG DAH 0.007068 0.42281 4.57831
31 5ML3 DL3 0.003455 0.45789 4.69799
32 5E4R NAP 0.02023 0.41037 4.79452
33 4XTX 590 0.02392 0.40789 4.81482
34 1B7Y FYA 0.000004666 0.44813 4.85714
35 2QHS OCA 0.007531 0.40697 5.48523
36 3IAA TYD 0.01566 0.40243 5.52885
37 3RSC TYD 0.01481 0.40708 5.54217
38 2J3M ATP 0.0000002662 0.64111 5.70776
39 2J3M PRI 0.0000003693 0.6368 5.70776
40 3HXU A5A 0.00000001191 0.55399 6.16438
41 2QHV OC9 0.004605 0.42175 6.19048
42 3O9L LPN 0.02135 0.41991 6.81818
43 2X4Z X4Z 0.0342 0.40328 7.09459
44 4L3L 5FI 0.01149 0.4228 7.23684
45 3R96 ACO 0.005727 0.44657 7.44681
46 3R96 AMP 0.005727 0.44657 7.44681
47 2I4O ATP 0.00000001588 0.67161 8.44749
48 4H2V AMP 0.0000009354 0.61175 10
49 2CM4 RCL 0.009782 0.41591 10
50 3IAL PR8 0.00002548 0.44612 10.274
51 12AS AMP 0.00000005626 0.68485 10.6061
52 4CS4 ANP 0.00000000003127 0.87397 14.5985
53 4CS4 AXZ 0.00000000005517 0.87397 14.5985
54 5A5W GUO 0.03101 0.41139 14.6245
55 3Q9L ATP 0.00991 0.40377 23.4615
56 3REU ATP 0.0000000000251 0.82196 39.4558
57 3A5Y KAA 0.000000001802 0.75353 40.5797
58 3G1Z AMP 0.0000000002321 0.75714 42.3313
59 3A5Z KAA 0.000000009908 0.71975 42.6829
60 2GU8 796 0.04437 0.41246 45
61 1E1O LYS 0.000004684 0.45015 45.8904
62 3BJU ATP 0.0000001596 0.63276 46.347
Pocket No.: 2; Query (leader) PDB : 3NEM; Ligand: AMO; Similar sites found: 57
This union binding pocket(no: 2) in the query (biounit: 3nem.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2ZTG A5A 0.000000001165 0.72084 1.82648
2 2CJ9 SSA 0.00000005253 0.54975 1.82648
3 2CJA ATP 0.000001713 0.48454 1.82648
4 3LGS ADE 0.03805 0.40109 2.24719
5 3QO8 SSA 0.00000005061 0.65538 2.28311
6 1WLE SRP 0.00000002958 0.56044 2.28311
7 5VAD 91Y 0.00008203 0.47751 2.28311
8 3ZJX BOG 0.03762 0.40229 2.76817
9 3UH0 TSB 0.00000607 0.5031 2.96804
10 3KYF 5GP 5GP 0.01834 0.40856 3.0303
11 1EM6 CP4 0.04026 0.40433 3.19635
12 4HWS 1B3 0.00003603 0.43069 3.40633
13 3ERR AMP 0.00001297 0.44645 3.42466
14 3CV2 COA 0.008649 0.43447 3.42466
15 5F7U GLC GLC 0.02152 0.41272 3.42466
16 3MEH THP 0.01574 0.40801 3.4965
17 1SES AHX 0.00000003988 0.66016 3.56295
18 1SES AMP 0.000003288 0.60338 3.56295
19 1JQN DCO 0.01717 0.40618 3.65297
20 4A91 GLU 0.02996 0.41153 3.69128
21 2CYB TYR 0.03908 0.40075 3.71517
22 4H2X G5A 0.0000001285 0.6204 3.8835
23 4H2W AMP 0.000001077 0.5939 3.8835
24 4H2W 5GP 0.00001642 0.53288 3.8835
25 5C5T AKG 0.02896 0.40239 3.94737
26 4HIA FMN 0.004746 0.40982 3.97727
27 4F8L AES 0.007135 0.44038 4.13793
28 3MF2 AMP 0.0000004475 0.5384 4.33526
29 5BVE 4VG 0.01699 0.40547 4.43213
30 3UN3 G16 0.01566 0.43224 4.51128
31 3TEG DAH 0.00001583 0.47821 4.57831
32 2RHQ GAX 0.001928 0.42424 4.79452
33 1B7Y FYA 0.0000001141 0.58166 4.85714
34 2J3M PRI 0.0000001706 0.56218 5.70776
35 2J3M ATP 0.0000001143 0.56202 5.70776
36 3HXU A5A 0.00000002958 0.62538 6.16438
37 4OYA 1VE 0.01658 0.40789 6.16438
38 2QHV OC9 0.00741 0.43274 6.19048
39 3A7R LAQ 0.003455 0.41666 6.23145
40 2E5A LAQ 0.002539 0.41296 6.91643
41 2VDF OCT 0.0003257 0.48631 7.50988
42 1SS4 GSH 0.00178 0.41093 7.84314
43 2ART LPA AMP 0.0001911 0.40284 8.39695
44 2I4O ATP 0.00000003205 0.50497 8.44749
45 4H2V AMP 0.0000002766 0.53909 10
46 1RL4 BRR 0.01401 0.4186 10.1064
47 3IAL PR8 0.000004506 0.53418 10.274
48 12AS AMP 0.0000000002529 0.68951 10.6061
49 4CS4 AXZ 0.00000000004386 0.7592 14.5985
50 4CS4 ANP 0.00000000002183 0.75896 14.5985
51 3G08 FEE 0.003857 0.42998 21.2121
52 3REU ATP 0.0000000002927 0.61422 39.4558
53 3A5Y KAA 0.00000000009322 0.69494 40.5797
54 3G1Z AMP 0.000000000876 0.55397 42.3313
55 3A5Z KAA 0.0000000003739 0.67979 42.6829
56 1E1O LYS 0.00000003098 0.60402 45.8904
57 3BJU ATP 0.00000052 0.49489 46.347
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