Receptor
PDB id Resolution Class Description Source Keywords
3A5Z 2.5 Å EC: 6.1.1.6 CRYSTAL STRUCTURE OF ESCHERICHIA COLI GENX IN COMPLEX WITH E FACTOR P ESCHERICHIA COLI AMINOACYL-TRNA SYNTHETASE PARALOG TRANSLATION TRNA LYSYL-SYNTHETASE ELONGATION FACTOR STRUCTURAL GENOMICS NPPSFAPROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES RIKESTRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI AMINOACYL-SYNTHETASE LIGASE
Ref.: A PARALOG OF LYSYL-TRNA SYNTHETASE AMINOACYLATES A LYSINE RESIDUE IN TRANSLATION ELONGATION FACTOR P. NAT.STRUCT.MOL.BIOL. V. 17 1136 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
KAA A:990;
C:991;
E:992;
G:993;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
474.492 C16 H26 N8 O7 S c1nc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3A5Z 2.5 Å EC: 6.1.1.6 CRYSTAL STRUCTURE OF ESCHERICHIA COLI GENX IN COMPLEX WITH E FACTOR P ESCHERICHIA COLI AMINOACYL-TRNA SYNTHETASE PARALOG TRANSLATION TRNA LYSYL-SYNTHETASE ELONGATION FACTOR STRUCTURAL GENOMICS NPPSFAPROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES RIKESTRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI AMINOACYL-SYNTHETASE LIGASE
Ref.: A PARALOG OF LYSYL-TRNA SYNTHETASE AMINOACYLATES A LYSINE RESIDUE IN TRANSLATION ELONGATION FACTOR P. NAT.STRUCT.MOL.BIOL. V. 17 1136 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 3A5Z - KAA C16 H26 N8 O7 S c1nc(c2c(n....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3A5Z - KAA C16 H26 N8 O7 S c1nc(c2c(n....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3A5Z - KAA C16 H26 N8 O7 S c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: KAA; Similar ligands found: 215
No: Ligand ECFP6 Tc MDL keys Tc
1 KAA 1 1
2 SSA 0.804598 0.942529
3 GSU 0.802198 0.942529
4 5CA 0.786517 0.942529
5 DSZ 0.769231 0.920455
6 LSS 0.769231 0.9
7 A5A 0.752809 0.908046
8 VMS 0.736264 0.88764
9 54H 0.736264 0.88764
10 TSB 0.728261 0.897727
11 53H 0.728261 0.877778
12 52H 0.717391 0.877778
13 YSA 0.707071 0.920455
14 NVA LMS 0.705263 0.9
15 G5A 0.7 0.965116
16 NSS 0.694737 0.920455
17 LEU LMS 0.680412 0.879121
18 XAH 0.673267 0.853933
19 WSA 0.669811 0.931035
20 5AS 0.633333 0.898876
21 LAD 0.623762 0.852273
22 P5A 0.607843 0.988506
23 4YB 0.558559 0.921348
24 649 0.552632 0.94382
25 AHX 0.542857 0.8
26 SON 0.541667 0.786517
27 CA0 0.536082 0.755556
28 7MD 0.535714 0.833333
29 5AL 0.534653 0.764045
30 A 0.532609 0.75
31 AMP 0.532609 0.75
32 5X8 0.530612 0.704545
33 SRP 0.524272 0.806818
34 DSH 0.521277 0.75
35 AMP MG 0.521277 0.714286
36 ADX 0.520408 0.863636
37 SLU 0.520325 0.868132
38 SA8 0.52 0.695652
39 ABM 0.515789 0.733333
40 A2D 0.515789 0.752809
41 SAH 0.514852 0.727273
42 SRA 0.510638 0.775281
43 AN2 0.510204 0.764045
44 YLP 0.508621 0.815217
45 5N5 0.505747 0.689655
46 AOC 0.505263 0.674157
47 A12 0.505155 0.766667
48 AP2 0.505155 0.766667
49 BA3 0.505155 0.752809
50 AU1 0.50505 0.755556
51 AMO 0.504673 0.786517
52 NB8 0.5 0.78022
53 5CD 0.5 0.659091
54 AP5 0.5 0.752809
55 B4P 0.5 0.752809
56 XYA 0.5 0.689655
57 ADP 0.5 0.752809
58 ME8 0.5 0.774194
59 RAB 0.5 0.689655
60 ADN 0.5 0.689655
61 TXA 0.5 0.747253
62 SFG 0.5 0.712644
63 YLB 0.495798 0.815217
64 YLC 0.495798 0.833333
65 8QN 0.495327 0.764045
66 GAP 0.495146 0.775281
67 S4M 0.494845 0.712766
68 3DH 0.494624 0.655556
69 AYB 0.491803 0.806452
70 M33 0.49 0.744444
71 ADP MG 0.49 0.725275
72 DAL AMP 0.485981 0.744444
73 SAI 0.485437 0.7
74 ADP BEF 0.485149 0.709677
75 50T 0.485149 0.725275
76 ACP 0.485149 0.755556
77 BEF ADP 0.485149 0.709677
78 ATP 0.485149 0.752809
79 YLA 0.483607 0.815217
80 EP4 0.483516 0.641304
81 7MC 0.483333 0.815217
82 A4D 0.483146 0.689655
83 K15 0.481818 0.691489
84 3UK 0.481818 0.755556
85 S7M 0.481132 0.698925
86 SMM 0.481132 0.694737
87 SAM 0.480769 0.698925
88 ANP 0.480769 0.755556
89 PRX 0.480392 0.736264
90 AQP 0.480392 0.752809
91 AR6 0.480392 0.752809
92 APC 0.480392 0.766667
93 APR 0.480392 0.752809
94 5FA 0.480392 0.752809
95 A7D 0.48 0.735632
96 GJV 0.479592 0.714286
97 6RE 0.479167 0.703297
98 DTA 0.478261 0.704545
99 WAQ 0.477477 0.808989
100 4AD 0.477064 0.777778
101 PAJ 0.477064 0.734043
102 EEM 0.47619 0.663158
103 ADP PO3 0.475728 0.75
104 RBY 0.475728 0.766667
105 SAP 0.475728 0.777778
106 AGS 0.475728 0.777778
107 AD9 0.475728 0.736264
108 ADV 0.475728 0.766667
109 ARG AMP 0.474576 0.784946
110 YAP 0.473684 0.777778
111 FA5 0.473684 0.786517
112 DLL 0.472727 0.764045
113 62X 0.472727 0.677083
114 ATF 0.471698 0.728261
115 ATP MG 0.471154 0.725275
116 J7C 0.469388 0.711111
117 OOB 0.46789 0.764045
118 ANP MG 0.46729 0.73913
119 ACQ 0.466667 0.755556
120 TAT 0.466667 0.766667
121 A3S 0.465347 0.724138
122 9SN 0.464912 0.723404
123 0UM 0.463636 0.725275
124 TYM 0.46281 0.786517
125 M2T 0.462366 0.645161
126 FYA 0.460177 0.764045
127 PTJ 0.460177 0.723404
128 1ZZ 0.460177 0.755319
129 BIS 0.460177 0.75
130 00A 0.459459 0.731183
131 A22 0.458716 0.744444
132 MAP 0.458716 0.73913
133 ADP ALF 0.457944 0.702128
134 ALF ADP 0.457944 0.702128
135 MTA 0.457447 0.655556
136 VRT 0.457143 0.711111
137 KB1 0.45614 0.688172
138 MYR AMP 0.45614 0.736842
139 OAD 0.455357 0.755556
140 N0B 0.454545 0.815217
141 A3N 0.454545 0.666667
142 5SV 0.454545 0.741935
143 25A 0.454545 0.752809
144 YLY 0.453846 0.806452
145 KH3 0.453782 0.702128
146 VO4 ADP 0.453704 0.744444
147 ADP VO4 0.453704 0.744444
148 IOT 0.451613 0.806452
149 PR8 0.451327 0.842697
150 ADQ 0.45045 0.755556
151 A1R 0.45045 0.808989
152 AAT 0.448598 0.733333
153 3OD 0.447368 0.755556
154 SXZ 0.447368 0.698925
155 JB6 0.447368 0.788889
156 MHZ 0.446602 0.723404
157 48N 0.446281 0.741935
158 MAO 0.445545 0.741935
159 A3G 0.444444 0.735632
160 TYR AMP 0.444444 0.747253
161 ADP BMA 0.442478 0.736264
162 A3T 0.442308 0.693182
163 TAD 0.441667 0.771739
164 AMP DBH 0.440678 0.698925
165 TXE 0.439024 0.75
166 ALF ADP 3PG 0.439024 0.715789
167 LA8 ALF 3PG 0.439024 0.715789
168 ZAS 0.438776 0.688889
169 LAQ 0.438017 0.793478
170 7C5 0.436975 0.677419
171 LPA AMP 0.434426 0.774194
172 25L 0.431034 0.744444
173 6V0 0.430894 0.741935
174 NEC 0.43 0.651685
175 GEK 0.428571 0.741573
176 S8M 0.428571 0.741573
177 4UV 0.428571 0.73913
178 OMR 0.427419 0.747368
179 A A 0.426087 0.733333
180 AR6 AR6 0.421488 0.733333
181 4UU 0.421488 0.73913
182 D3Y 0.419643 0.707865
183 TXD 0.419355 0.75
184 DND 0.419355 0.747253
185 NAX 0.419355 0.763441
186 NXX 0.419355 0.747253
187 SO8 0.416667 0.67033
188 AF3 ADP 3PG 0.416 0.715789
189 COD 0.415385 0.808511
190 2VA 0.415094 0.677778
191 AHZ 0.414634 0.71875
192 3AM 0.414141 0.738636
193 T5A 0.414062 0.739583
194 3NZ 0.413793 0.703297
195 ATP A A A 0.411765 0.741573
196 5AD 0.411111 0.609195
197 AFH 0.409836 0.734043
198 7D5 0.408163 0.722222
199 UP5 0.408 0.73913
200 4UW 0.408 0.715789
201 NAI 0.408 0.731183
202 NAD IBO 0.407692 0.72043
203 A5D 0.407407 0.704545
204 7D7 0.406593 0.647727
205 GTA 0.406504 0.701031
206 4TA 0.40458 0.729167
207 A3P 0.403846 0.75
208 A2P 0.403846 0.738636
209 594 0.402985 0.864583
210 G3A 0.401639 0.723404
211 4TC 0.401575 0.741935
212 BT5 0.401515 0.787234
213 V3L 0.4 0.752809
214 67D 0.4 0.9
215 CNA 0.4 0.766667
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3A5Z; Ligand: KAA; Similar sites found: 100
This union binding pocket(no: 1) in the query (biounit: 3a5z.bio2) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2ART LPA AMP 0.00005131 0.42218 2.29008
2 3TEG DAH 0.00001593 0.51646 2.43902
3 3HXU A5A 0.00000000175 0.67668 2.6178
4 1VJ7 GPX 0.0247 0.41272 3.04878
5 4HWS 1B3 0.00004491 0.428 3.14136
6 4FFG 0U8 0.01718 0.423 3.14136
7 5D9G GLU ASN LEU TYR PHE GLN 0.02603 0.40477 3.25203
8 4XMF HSM 0.01979 0.40594 3.26087
9 2VDF OCT 0.00001252 0.57703 3.55731
10 1WLE SRP 0.000000351 0.52494 3.66492
11 1RYD GLC 0.01223 0.4309 3.66492
12 1A5Z FBP 0.03666 0.40098 3.66492
13 5H2U 1N1 0.01693 0.40286 4.11985
14 4D4U FUC GAL NDG FUC 0.01286 0.41628 4.12698
15 3GD9 GLC BGC BGC BGC 0.007024 0.42509 4.18848
16 1M5W DXP 0.03031 0.40538 4.18848
17 1MFI FHC 0.02594 0.412 4.38596
18 4NS0 PIO 0.006512 0.44251 4.51128
19 3CM2 X23 0.03348 0.40309 4.61538
20 2E5A LAQ 0.0006236 0.42246 4.71204
21 3ACL 3F1 0.007848 0.41499 4.71204
22 3KRQ 3TR 0.02871 0.4118 4.71204
23 3EFS BTN 0.004967 0.41686 4.72103
24 3ESS 18N 0.04271 0.4013 4.78261
25 4IAW LIZ 0.02437 0.40237 4.78723
26 3T4L ZEA 0.001074 0.45061 4.81482
27 1RZX ACE VAL LYS GLU SER LEU VAL 0.008796 0.43708 5.10204
28 3MF2 AMP 0.000001593 0.55305 5.2356
29 2G30 ALA ALA PHE 0.0002092 0.49173 5.2356
30 4G0P U5P 0.01878 0.41433 5.44218
31 3UH0 TSB 0.00001741 0.48618 5.75916
32 5MRH Q9Z 0.03082 0.40099 5.75916
33 2RHQ GAX 0.0003888 0.4533 5.78231
34 4HWT 1B2 0.0004577 0.41776 6.09756
35 3SJK LYS PRO VAL LEU ARG THR ALA 0.03462 0.40817 6.31579
36 4IEN GDP 0.0009857 0.45677 6.74847
37 3QO8 SSA 0.0000001838 0.62945 6.80628
38 1B7Y FYA 0.00000002028 0.61129 6.80628
39 4MOB ADP 0.00002713 0.56971 6.80628
40 2Y91 98J 0.03066 0.40593 6.80628
41 3QH2 3NM 0.0337 0.40293 6.80628
42 4K30 NLG 0.01998 0.4067 6.875
43 5VAD PRO 0.001749 0.44968 7.0122
44 5VAD 91Y 0.0003617 0.42026 7.0122
45 3QX9 ATP 0.006476 0.44331 7.24638
46 12AS AMP 0.00000001691 0.61704 7.32984
47 3KYF 5GP 5GP 0.007303 0.42852 7.32984
48 2A9W UMP 0.03145 0.40492 7.32984
49 3DWQ NGC GAL NGA POL AZI 0.01015 0.43421 7.93651
50 1UNQ 4IP 0.03155 0.40503 8
51 2GGX NPJ 0.02806 0.40722 8.125
52 1OPB RET 0.005476 0.41497 8.20895
53 1A78 TDG 0.03889 0.40131 8.20895
54 3UEC ALA ARG TPO LYS 0.01115 0.43556 8.21918
55 2CJ9 SSA 0.000001944 0.50093 8.37696
56 2CJA ATP 0.0001259 0.49816 8.37696
57 2QHV OC9 0.003427 0.44982 8.37696
58 3A16 PXO 0.00374 0.4503 8.84146
59 5F7U GLC GLC 0.005705 0.44691 8.84146
60 5T96 79J 0.0398 0.40236 8.84146
61 4DSU BZI 0.005929 0.44667 9.14634
62 2QHS OCA 0.004801 0.43759 9.2827
63 2YKL NLD 0.01142 0.41482 9.42408
64 3SAO DBH 0.0279 0.40753 10
65 3IAL PR8 0.00000618 0.52845 10.061
66 3HCH RSM 0.02286 0.41271 10.274
67 4DS0 A2G GAL NAG FUC 0.01865 0.42652 10.4294
68 5F7Y GLC GAL NAG GAL FUC A2G 0.01569 0.40808 11.5183
69 2H7C SIA 0.01587 0.41749 11.5854
70 2J3M ATP 0.0000001619 0.59453 12.0419
71 2J3M PRI 0.0000002908 0.57756 12.0419
72 4PQG NAG 0.01163 0.42273 12.0419
73 3CBC DBS 0.01673 0.42625 12.1212
74 2I4O ATP 0.00000005328 0.6835 12.5654
75 2GQS C2R 0.01429 0.40637 12.5654
76 5M6N 7H9 0.03581 0.40188 12.7119
77 3REU ATP 0.00000001384 0.67216 12.9252
78 4MTI 2DX 0.02766 0.40846 13.0435
79 2BVE PH5 0.02417 0.4234 13.4454
80 2ZTG A5A 0.000000008681 0.68134 13.6126
81 4K55 H6P 0.01835 0.41785 14.5161
82 4H2X G5A 0.000000844 0.58414 14.5631
83 4H2W AMP 0.00000847 0.55243 14.5631
84 4H2W 5GP 0.00004673 0.5123 14.5631
85 3H0L ADP 0.01647 0.41499 14.8936
86 4RHS SIA SIA GAL 0.002267 0.47873 15.5738
87 3IWD M2T 0.02046 0.41612 16.1765
88 4CS4 AXZ 0.0000000001119 0.74198 17.1533
89 4CS4 ANP 0.00000000005604 0.74198 17.1533
90 1SES AHX 0.0000001951 0.62825 17.801
91 1SES AMP 0.00004766 0.54431 17.801
92 3ERR AMP 0.00004525 0.42779 17.801
93 3QPB URA 0.02894 0.40529 18.8482
94 4H2V AMP 0.0000009105 0.52502 20
95 1OFL NGK GCD 0.004539 0.44443 20.9424
96 1G51 AMO 0.0000000004177 0.68086 23.1707
97 2XGT NSS 0.0000000002169 0.67619 35.3659
98 1X54 4AD 0.0000000006555 0.66207 36.2805
99 3NEM ATP 0.000000009908 0.71975 42.6829
100 3NEM AMO 0.0000000003739 0.67979 42.6829
Pocket No.: 2; Query (leader) PDB : 3A5Z; Ligand: KAA; 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: 3a5z.bio2) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3A5Z; Ligand: KAA; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3a5z.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3A5Z; Ligand: KAA; Similar sites found: 30
This union binding pocket(no: 4) in the query (biounit: 3a5z.bio1) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4NOS ITU 0.03621 0.40115 2.6178
2 1LTZ HBI 0.03737 0.40433 3.66492
3 2C5S AMP 0.03218 0.40384 3.66492
4 5DMZ ADP 0.009198 0.4091 4.26829
5 2J5V RGP 0.03373 0.40628 4.26829
6 5M0T AKG 0.03776 0.40666 4.7619
7 2CYC TYR 0.03534 0.40769 4.87805
8 3KYG 5GP 5GP 0.01005 0.40735 5.2356
9 3QXQ CE5 0.02526 0.40184 5.2356
10 1WOG 16D 0.02569 0.41472 5.2459
11 1BC5 ACE ASN TRP GLU THR PHE 0.02705 0.40778 5.57621
12 2WGV CIT 0.02233 0.41697 5.64516
13 2CYB TYR 0.02786 0.41245 5.75916
14 1NJJ GET 0.0187 0.4121 5.75916
15 1GPM AMP 0.04155 0.40271 5.75916
16 4BC5 5FX 0.02659 0.40097 5.79268
17 3CV2 COA 0.02758 0.41486 6.28272
18 4R38 RBF 0.01141 0.40177 6.42857
19 3A7R LAQ 0.0006508 0.40124 6.70732
20 1V84 UDP 0.02033 0.41424 6.71937
21 2HZQ STR 0.02769 0.41351 6.89655
22 5EW9 5VC 0.01651 0.41667 7.01107
23 3JQ3 ADP 0.02781 0.40335 7.8534
24 1FHX 4IP 0.01817 0.42109 9.30233
25 4YVN EBS 0.006517 0.44692 11.2805
26 3LXR GDP 0.02336 0.40007 11.8919
27 1SW0 PGA 0.02025 0.40661 13.089
28 4AVV GHE 0.04374 0.40054 15.7068
29 1SVI GDP 0.03795 0.40008 20
30 3MEH THP 0.02522 0.40188 32.1678
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