Receptor
PDB id Resolution Class Description Source Keywords
2DXU 1.28 Å EC: 6.3.4.15 CRYSTAL STRUCTURE OF BIOTIN PROTEIN LIGASE FROM PYROCOCCUS HORIKOSHII COMPLEXED WITH BIOTINYL-5'-AMP, MUTATION R48A PYROCOCCUS HORIKOSHII BIOTIN BIOSYNTHESIS DIMER X-RAY DIFFRACTION STRUCTURAL GENOMICS NPPSFA NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI LIGASE
Ref.: PROTEIN BIOTINYLATION VISUALIZED BY A COMPLEX STRUCTURE OF BIOTIN PROTEIN LIGASE WITH A SUBSTRATE J.BIOL.CHEM. V. 283 14739 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BT5 B:2301;
B:2302;
Valid;
Valid;
none;
none;
submit data
573.517 C20 H28 N7 O9 P S c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2DXU 1.28 Å EC: 6.3.4.15 CRYSTAL STRUCTURE OF BIOTIN PROTEIN LIGASE FROM PYROCOCCUS HORIKOSHII COMPLEXED WITH BIOTINYL-5'-AMP, MUTATION R48A PYROCOCCUS HORIKOSHII BIOTIN BIOSYNTHESIS DIMER X-RAY DIFFRACTION STRUCTURAL GENOMICS NPPSFA NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI LIGASE
Ref.: PROTEIN BIOTINYLATION VISUALIZED BY A COMPLEX STRUCTURE OF BIOTIN PROTEIN LIGASE WITH A SUBSTRATE J.BIOL.CHEM. V. 283 14739 2008
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 2DXU - BT5 C20 H28 N7 O9 P S c1nc(c2c(n....
2 1WQW - BT5 C20 H28 N7 O9 P S c1nc(c2c(n....
3 1WNL - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
4 1X01 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
5 2E41 - BTX C20 H30 N7 O8 P S c1nc(c2c(n....
6 2ZGW - BTN C10 H16 N2 O3 S C1[C@H]2[C....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 2DXU - BT5 C20 H28 N7 O9 P S c1nc(c2c(n....
2 1WQW - BT5 C20 H28 N7 O9 P S c1nc(c2c(n....
3 1WNL - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
4 1X01 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
5 2E41 - BTX C20 H30 N7 O8 P S c1nc(c2c(n....
6 2ZGW - BTN C10 H16 N2 O3 S C1[C@H]2[C....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 2DXU - BT5 C20 H28 N7 O9 P S c1nc(c2c(n....
2 1WQW - BT5 C20 H28 N7 O9 P S c1nc(c2c(n....
3 1WNL - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
4 1X01 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
5 2E41 - BTX C20 H30 N7 O8 P S c1nc(c2c(n....
6 2ZGW - BTN C10 H16 N2 O3 S C1[C@H]2[C....
7 3EFS Kd = 7.2 uM ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: BT5; Similar ligands found: 218
No: Ligand ECFP6 Tc MDL keys Tc
1 BT5 1 1
2 BTX 0.782609 0.987805
3 BS5 0.663934 0.827957
4 1ZZ 0.660714 0.850575
5 LAQ 0.652542 0.916667
6 WAQ 0.651786 0.914634
7 8LQ 0.59292 0.845238
8 594 0.583333 0.822917
9 CA0 0.574074 0.833333
10 KG4 0.568807 0.833333
11 44L 0.568182 0.793814
12 DLL 0.564103 0.843373
13 A2D 0.556604 0.809524
14 TXA 0.55 0.823529
15 590 0.55 0.833333
16 OOB 0.547009 0.843373
17 8LE 0.54386 0.813953
18 5AL 0.54386 0.843373
19 44Q 0.541353 0.836957
20 50T 0.540541 0.8
21 00A 0.537815 0.804598
22 44M 0.535714 0.793814
23 ANP 0.535088 0.811765
24 8LH 0.534483 0.823529
25 SRP 0.534483 0.86747
26 8QN 0.533898 0.843373
27 MYR AMP 0.532787 0.829545
28 BA3 0.53211 0.809524
29 LPA AMP 0.53125 0.894118
30 PAJ 0.529412 0.786517
31 A3R 0.529412 0.847059
32 AMO 0.529412 0.86747
33 PR8 0.528926 0.904762
34 ADP 0.527273 0.831325
35 AP5 0.527273 0.809524
36 B4P 0.527273 0.809524
37 NB8 0.52459 0.837209
38 OMR 0.523077 0.840909
39 AN2 0.522523 0.821429
40 AT4 0.522523 0.845238
41 AR6 0.522124 0.831325
42 APR 0.522124 0.831325
43 OAD 0.520661 0.833333
44 3UK 0.520661 0.833333
45 44N 0.517986 0.842105
46 ADX 0.517857 0.758242
47 M33 0.517857 0.8
48 SAP 0.517544 0.835294
49 AGS 0.517544 0.835294
50 4AD 0.516667 0.857143
51 LAD 0.516393 0.892857
52 B5V 0.516393 0.823529
53 A 0.514019 0.829268
54 AMP 0.514019 0.829268
55 ACP 0.513274 0.833333
56 HEJ 0.513274 0.831325
57 ATP 0.513274 0.831325
58 ATF 0.512821 0.802326
59 AHX 0.512397 0.816092
60 ME8 0.512195 0.850575
61 PTJ 0.512195 0.816092
62 BIS 0.512195 0.825581
63 YAP 0.512 0.857143
64 IOT 0.511278 0.885057
65 SON 0.508929 0.890244
66 5FA 0.508772 0.831325
67 AQP 0.508772 0.831325
68 PRX 0.508772 0.811765
69 AD9 0.504348 0.811765
70 A1R 0.504132 0.847059
71 9SN 0.504 0.795455
72 FA5 0.5 0.86747
73 TYM 0.5 0.86747
74 3OD 0.5 0.833333
75 B5M 0.5 0.813953
76 ABM 0.5 0.788235
77 45A 0.5 0.788235
78 B5Y 0.5 0.813953
79 4UU 0.496124 0.813953
80 9X8 0.495935 0.835294
81 5SV 0.495868 0.816092
82 GAP 0.495726 0.811765
83 ACQ 0.495726 0.833333
84 44O 0.492857 0.8125
85 NAI 0.492424 0.784091
86 4UV 0.492188 0.813953
87 HQG 0.491667 0.843373
88 AU1 0.491228 0.811765
89 A12 0.491071 0.845238
90 AP2 0.491071 0.845238
91 44K 0.489051 0.76087
92 A22 0.487603 0.821429
93 YLB 0.485075 0.873563
94 YLP 0.484848 0.873563
95 XAH 0.484375 0.850575
96 6YZ 0.483333 0.833333
97 ADP MG 0.482456 0.807229
98 SRA 0.481818 0.833333
99 4UW 0.481203 0.786517
100 NXX 0.481203 0.823529
101 NAX 0.481203 0.818182
102 DND 0.481203 0.823529
103 YLY 0.478873 0.863636
104 FYA 0.47619 0.843373
105 MAP 0.47541 0.793103
106 COD 0.47482 0.844444
107 YLC 0.474074 0.872093
108 48N 0.473684 0.816092
109 9ZA 0.471545 0.825581
110 OZV 0.471545 0.831325
111 9ZD 0.471545 0.825581
112 25A 0.471545 0.831325
113 AYB 0.471014 0.863636
114 T99 0.470588 0.845238
115 TAT 0.470588 0.845238
116 APC 0.470085 0.845238
117 DQV 0.469697 0.821429
118 ADQ 0.467742 0.811765
119 44R 0.466667 0.776596
120 TXE 0.466667 0.804598
121 RBY 0.466102 0.845238
122 ADV 0.466102 0.845238
123 APC MG 0.466102 0.809524
124 G3A 0.465649 0.795455
125 YLA 0.463768 0.873563
126 T5A 0.463768 0.831461
127 DAL AMP 0.463415 0.821429
128 G5P 0.462121 0.795455
129 7MD 0.462121 0.872093
130 CNA 0.460432 0.823529
131 TXD 0.459259 0.804598
132 6V0 0.459259 0.775281
133 GTA 0.458647 0.769231
134 F2R 0.457143 0.852273
135 NAD 0.453901 0.821429
136 ATP MG 0.453782 0.807229
137 ADP PO3 0.453782 0.807229
138 AP0 0.452555 0.755556
139 GA7 0.451128 0.781609
140 AFH 0.451128 0.786517
141 DZD 0.450704 0.827586
142 25L 0.449612 0.821429
143 A4P 0.449275 0.755319
144 H1Q 0.449153 0.776471
145 N0B 0.44898 0.873563
146 A3D 0.447552 0.811765
147 ADP VO4 0.447154 0.8
148 VO4 ADP 0.447154 0.8
149 AMP DBH 0.44697 0.770115
150 TYR AMP 0.44697 0.835294
151 139 0.442857 0.83908
152 ADJ 0.442857 0.820225
153 7MC 0.442029 0.852273
154 BQX 0.441176 0.72043
155 ARG AMP 0.440298 0.840909
156 ALF ADP 0.439024 0.752809
157 ADP ALF 0.439024 0.752809
158 UP5 0.437956 0.813953
159 TAD 0.437037 0.870588
160 LMS 0.433628 0.73913
161 UPA 0.431655 0.804598
162 4TC 0.431655 0.816092
163 JB6 0.430769 0.869048
164 TSB 0.428571 0.734043
165 M24 0.428571 0.777778
166 8X1 0.428571 0.75
167 80F 0.427586 0.831461
168 G5A 0.42623 0.755319
169 AOC 0.426087 0.705882
170 SSA 0.424 0.755319
171 5AS 0.423729 0.71875
172 P5A 0.423077 0.797872
173 A A 0.423077 0.809524
174 NAQ 0.422819 0.775281
175 9JJ 0.421687 0.75
176 52H 0.420635 0.71875
177 54H 0.420635 0.726316
178 VMS 0.420635 0.726316
179 53H 0.417323 0.71875
180 A5A 0.416 0.741935
181 ADP BMA 0.415385 0.790698
182 EAD 0.414474 0.777778
183 AF3 ADP 3PG 0.414286 0.786517
184 649 0.414286 0.797872
185 AMP NAD 0.413793 0.821429
186 0WD 0.413793 0.795455
187 AHZ 0.413043 0.829545
188 NDE 0.412903 0.823529
189 P1H 0.412903 0.78022
190 DSZ 0.410853 0.774194
191 ATP A 0.410448 0.797619
192 ATP A A A 0.410448 0.797619
193 8PZ 0.410448 0.755319
194 2A5 0.409836 0.833333
195 NDC 0.407643 0.858824
196 YSA 0.407407 0.755319
197 GJV 0.40678 0.727273
198 NAE 0.406667 0.793103
199 PAP 0.406504 0.819277
200 5CA 0.40625 0.755319
201 6RE 0.405172 0.715909
202 NA7 0.40458 0.86747
203 WSA 0.404255 0.763441
204 4TA 0.40411 0.820225
205 A4D 0.40367 0.702381
206 5CD 0.40367 0.690476
207 A3P 0.403361 0.829268
208 FNK 0.402439 0.778947
209 XYA 0.401869 0.702381
210 RAB 0.401869 0.702381
211 ADN 0.401869 0.702381
212 KAA 0.401515 0.787234
213 GSU 0.401515 0.793478
214 7C5 0.40146 0.747126
215 ZID 0.401316 0.811765
216 LSS 0.4 0.739583
217 3AM 0.4 0.795181
218 NSS 0.4 0.755319
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2DXU; Ligand: BT5; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2dxu.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2DXU; Ligand: BT5; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2dxu.bio1) has 34 residues
No: Leader PDB Ligand Sequence Similarity
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