-->
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;
submit data
133.103 C4 H7 N O4 C([C@...
View in 3D viewer
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 2 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 DAS 1 1
2 ASP 1 1
3 ASN 0.636364 0.793103
4 DSN 0.545455 0.714286
5 ABA 0.545455 0.692308
6 2RA 0.545455 0.689655
7 SER 0.545455 0.714286
8 DBB 0.545455 0.692308
9 CYS 0.521739 0.703704
10 C2N 0.521739 0.666667
11 DCY 0.521739 0.703704
12 SD4 0.5 0.648649
13 GGL 0.481481 0.846154
14 DGL 0.481481 0.846154
15 GLU 0.481481 0.846154
16 DAB 0.48 0.612903
17 HSE 0.48 0.758621
18 NVA 0.461538 0.62069
19 HCS 0.461538 0.655172
20 CSO 0.461538 0.6875
21 AS2 0.461538 0.916667
22 LEU 0.461538 0.642857
23 API 0.461538 0.75
24 CSD 0.444444 0.615385
25 CSS 0.444444 0.633333
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 with APoc: 87
This union binding pocket(no: 1) in the query (biounit: 3nem.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 1ZEI CRS None
2 3KB6 NAD 1.49701
3 5UIU 8CG 1.54799
4 2ZTG A5A 1.82648
5 2CJ9 SSA 1.82648
6 2CJA ATP 1.82648
7 5V59 8X1 1.82648
8 4DQ2 BTX 2.13415
9 1WLE SRP 2.28311
10 3QO8 SSA 2.28311
11 5VAD 91Y 2.28311
12 2JLB UDM 2.51142
13 2DXU BT5 2.55319
14 4TSK NDP 2.57143
15 1PN0 FAD 2.73973
16 1PN0 IPH 2.73973
17 5TA6 79D 2.7933
18 3UH0 TSB 2.96804
19 6B3V 7DQ 3.15789
20 4YDQ ANP 3.19635
21 4YDQ HFG 3.19635
22 3E8N VRA 3.22581
23 3E8N ATP 3.22581
24 4IQY AR6 3.33333
25 4HWS 1B3 3.40633
26 3ERR AMP 3.42466
27 3CV2 COA 3.42466
28 1Q19 APC 3.42466
29 3MVH WFE 3.50877
30 5N87 N66 3.51438
31 1SES AMP 3.56295
32 1SES AHX 3.56295
33 2JLD AG1 3.57143
34 2Y88 2ER 3.68852
35 4XDZ NDP 3.79009
36 4H2W AMP 3.8835
37 4H2X G5A 3.8835
38 4H2W 5GP 3.8835
39 3MF2 AMP 4.33526
40 3TEG DAH 4.57831
41 5ML3 DL3 4.69799
42 5E4R NAP 4.79452
43 4XTX 590 4.81482
44 1B7Y FYA 4.85714
45 4N70 2HX 4.87805
46 5XIO ANP 5.02283
47 1KDK DHT 5.08475
48 4ZTD ALA GLY ALA GLY ALA 5.13834
49 4YRI 4JH 5.47945
50 4FL3 ANP 5.47945
51 2QHS OCA 5.48523
52 3IAA TYD 5.52885
53 3RSC TYD 5.54217
54 2J3M ATP 5.70776
55 2J3M PRI 5.70776
56 6FFK D7Z 5.88235
57 6G9I CXX 5.95238
58 3HXU A5A 6.16438
59 2QHV OC9 6.19048
60 1JG3 ADN 6.38298
61 3O9L LPN 6.81818
62 6C0T EE4 6.91643
63 1N62 FAD 6.94444
64 4L3L 5FI 7.23684
65 3R96 ACO 7.44681
66 3R96 AMP 7.44681
67 2ART LPA AMP 8.39695
68 2I4O ATP 8.44749
69 5XIJ ANP 8.44749
70 5XIJ 873 8.44749
71 3VPB ADP 8.86525
72 4H2V AMP 10
73 2CM4 RCL 10
74 3IAL PR8 10.274
75 12AS AMP 10.6061
76 3NRR D16 11.4155
77 4CS4 ANP 14.5985
78 4CS4 AXZ 14.5985
79 5A5W GUO 14.6245
80 3Q9L ATP 23.4615
81 3REU ATP 39.4558
82 3A5Y KAA 40.5797
83 3G1Z AMP 42.3313
84 3A5Z KAA 42.6829
85 2GU8 796 45
86 1E1O LYS 45.8904
87 3BJU ATP 46.347
Pocket No.: 2; Query (leader) PDB : 3NEM; Ligand: AMO; Similar sites found with APoc: 171
This union binding pocket(no: 2) in the query (biounit: 3nem.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 1ZEI CRS None
2 4CQK PIO None
3 2BOS GLA GAL GLC None
4 2BOS GLA GAL None
5 1W96 S1A 1.14155
6 5W75 SUC 1.27551
7 4MOB ADP 1.50602
8 5YJS SAL 1.53846
9 4YVN EBS 1.59817
10 5H9Y BGC BGC BGC BGC 1.59817
11 1KC7 PPR 1.59817
12 3HQP OXL 1.59817
13 4X1Z FUC GAL NDG 1.80723
14 5V59 8X1 1.82648
15 2ZTG A5A 1.82648
16 2CJ9 SSA 1.82648
17 2CJA ATP 1.82648
18 1QHO MAL 1.82648
19 5DBX ANP 1.82927
20 1IZC PYR 2.0649
21 1NJJ GET 2.11765
22 3LGS ADE 2.24719
23 1WLE SRP 2.28311
24 3QO8 SSA 2.28311
25 5VAD 91Y 2.28311
26 5VAD PRO 2.28311
27 1F9V ADP 2.30548
28 1UPR 4IP 2.43902
29 1M5W DXP 2.46914
30 5E6O TRP GLU GLU LEU 2.54237
31 5H2U 1N1 2.62172
32 3NZ1 3NY 2.68199
33 3GD8 GOL 2.69058
34 4WOE ADP 2.73973
35 5DMZ ADP 2.73973
36 3ZJX BOG 2.76817
37 5KJW 53C 2.8103
38 5EJL C2E 2.82258
39 3F5A SIA GAL NAG 2.84553
40 5G48 1FL 2.94118
41 3UH0 TSB 2.96804
42 1VBH PEP 2.96804
43 4RF7 ARG 2.96804
44 1PCA CIT 2.97767
45 3KYF 5GP 5GP 3.0303
46 1W8S FBP 3.04183
47 3CM2 X23 3.07692
48 2XZ9 PYR 3.08642
49 5OQW A4E 3.14961
50 1SDW IYT 3.18471
51 4YDQ HFG 3.19635
52 4YDQ ANP 3.19635
53 4CPB GAL CN8 3.30579
54 6EWZ APC 3.37553
55 4HWS 1B3 3.40633
56 3ERR AMP 3.42466
57 3CV2 COA 3.42466
58 5F7U GLC GLC 3.42466
59 1YFS ALA 3.42466
60 3MEH THP 3.4965
61 2HJ9 AI2 3.53982
62 1SES AHX 3.56295
63 1SES AMP 3.56295
64 1JQN DCO 3.65297
65 4A91 GLU 3.69128
66 1H3F TYE 3.7037
67 2CYB TYR 3.71517
68 3QSB 743 3.82514
69 4H2X G5A 3.8835
70 4H2W AMP 3.8835
71 4H2W 5GP 3.8835
72 1F5F DHT 3.90244
73 5C5T AKG 3.94737
74 4HIA FMN 3.97727
75 4G0P U5P 4.08163
76 4HWT 1B2 4.11622
77 4F8L AES 4.13793
78 4ZS4 ATP 4.23453
79 3UW5 MAA CHG PRO 0DQ 4.31034
80 3MF2 AMP 4.33526
81 3UN3 G16 4.51128
82 4RYV ZEA 4.51613
83 3A16 PXO 4.55764
84 3TEG DAH 4.57831
85 6FA4 D1W 4.62428
86 1FDJ 13P 4.6832
87 3EFS BTN 4.72103
88 4D52 GXL 4.7619
89 4D52 GIV 4.7619
90 2RHQ GAX 4.79452
91 1B7Y FYA 4.85714
92 2Z3U CRR 4.94118
93 5XIO ANP 5.02283
94 5XIO HFG 5.02283
95 2PNC CLU 5.02283
96 4ZTD ALA GLY ALA GLY ALA 5.13834
97 6GNO XDI 5.18518
98 1HXD BTN 5.29595
99 4AVV CD 5.39216
100 4AVV GHE 5.39216
101 4YRI 4JH 5.47945
102 2QHS OCA 5.48523
103 2J3M ATP 5.70776
104 2J3M PRI 5.70776
105 1OFZ FUC 5.76923
106 5WHT SIA GAL 5.7971
107 5WHT SIA GAL GLC 5.7971
108 5WHT SIA 5.7971
109 3DXY SAM 5.9633
110 5LHT TIH 6.12245
111 1RZX ACE VAL LYS GLU SER LEU VAL 6.12245
112 3HXU A5A 6.16438
113 4OYA 1VE 6.16438
114 2QHV OC9 6.19048
115 5XNC N4P 6.19946
116 1NX4 AKG 6.22711
117 3A7R LAQ 6.23145
118 1GPM AMP 6.39269
119 4K7O EKZ 6.54762
120 4RHS SIA SIA GAL 6.55738
121 3KIF GDL 6.60377
122 2J5B TYE 6.6092
123 1WOG 16D 6.84932
124 2E5A LAQ 6.91643
125 5WL1 D3D 7.07071
126 5WL1 CUY 7.07071
127 4LRJ ANP 7.10059
128 2OJW ADP 7.29167
129 2VDF OCT 7.50988
130 6E1Q CFA 7.53425
131 5FUI APY 7.57576
132 3UW4 MAA CHG PRO 0DQ 7.6087
133 6FLZ MMA 7.63889
134 5HWV MBN 7.69231
135 1KHT AMP 7.8125
136 1SS4 GSH 7.84314
137 1R1Q ACE ARG GLU PTR VAL ASN VAL 8
138 5H9P TD2 8.22785
139 2ART LPA AMP 8.39695
140 2I4O ATP 8.44749
141 5XIJ ANP 8.44749
142 5XIJ 873 8.44749
143 5LXT GTP 8.44749
144 4WQQ MAN 8.51064
145 2J9L ATP 8.64865
146 1VRP ADP 8.66142
147 4H2V AMP 10
148 1RL4 BRR 10.1064
149 5M6N 7H9 10.1695
150 3IAL PR8 10.274
151 12AS AMP 10.6061
152 6DZN AE3 10.7981
153 1U29 I3P 11.6279
154 4MTI 2DX 12.1739
155 2YKL NLD 12.2642
156 2GQS C2R 12.6582
157 4P9Z NMI PTR 02K ASN NH2 12.8205
158 3T4L ZEA 12.963
159 2BVE PH5 13.4454
160 3WD6 GSH 14.0625
161 4CS4 ANP 14.5985
162 4CS4 AXZ 14.5985
163 5VM6 9EG 21.1679
164 3G08 FEE 21.2121
165 1QO0 BMD 21.9388
166 3REU ATP 39.4558
167 3A5Y KAA 40.5797
168 3G1Z AMP 42.3313
169 3A5Z KAA 42.6829
170 1E1O LYS 45.8904
171 3BJU ATP 46.347
APoc FAQ
Feedback