Receptor
PDB id Resolution Class Description Source Keywords
1WQW 1.45 Å EC: 6.3.4.15 CRYSTAL STRUCTURE OF BIOTIN PROTEIN LIGASE FROM PYROCOCCUS H OT3 IN COMPLEX WITH BIOTINYL-5-AMP PYROCOCCUS HORIKOSHII BIOTIN PROTEIN LIGASE DIMER STRUCTURAL GENOMICS RIKEN STRGENOMICS/PROTEOMICS INITIATIVE RSGI LIGASE
Ref.: CRYSTAL STRUCTURES OF BIOTIN PROTEIN LIGASE FROM PY HORIKOSHII OT3 AND ITS COMPLEXES: STRUCTURAL BASIS ACTIVATION J.MOL.BIOL. V. 353 322 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BT5 A:1301;
B:1302;
 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 (2D)
Ligand no: 1; Ligand: BT5; Similar ligands found: 224
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 QA7 0.551724 0.813953
15 590 0.55 0.833333
16 TXA 0.55 0.823529
17 OOB 0.547009 0.843373
18 8LE 0.54386 0.813953
19 5AL 0.54386 0.843373
20 44Q 0.541353 0.836957
21 50T 0.540541 0.8
22 00A 0.537815 0.804598
23 44M 0.535714 0.793814
24 ANP 0.535088 0.811765
25 8LH 0.534483 0.823529
26 SRP 0.534483 0.86747
27 8QN 0.533898 0.843373
28 MYR AMP 0.532787 0.829545
29 BA3 0.53211 0.809524
30 LPA AMP 0.53125 0.894118
31 AMO 0.529412 0.86747
32 PAJ 0.529412 0.786517
33 A3R 0.529412 0.847059
34 PR8 0.528926 0.904762
35 B4P 0.527273 0.809524
36 AP5 0.527273 0.809524
37 ADP 0.527273 0.831325
38 NB8 0.52459 0.837209
39 OMR 0.523077 0.840909
40 AT4 0.522523 0.845238
41 AN2 0.522523 0.821429
42 APR 0.522124 0.831325
43 AR6 0.522124 0.831325
44 OAD 0.520661 0.833333
45 3UK 0.520661 0.833333
46 44N 0.517986 0.842105
47 ADX 0.517857 0.758242
48 M33 0.517857 0.8
49 AGS 0.517544 0.835294
50 4AD 0.516667 0.857143
51 B5V 0.516393 0.823529
52 LAD 0.516393 0.892857
53 A 0.514019 0.829268
54 AMP 0.514019 0.829268
55 ATP 0.513274 0.831325
56 ACP 0.513274 0.833333
57 HEJ 0.513274 0.831325
58 ATF 0.512821 0.802326
59 AHX 0.512397 0.816092
60 ME8 0.512195 0.850575
61 BIS 0.512195 0.825581
62 PTJ 0.512195 0.816092
63 IOT 0.511278 0.885057
64 SON 0.508929 0.890244
65 PRX 0.508772 0.811765
66 AQP 0.508772 0.831325
67 5FA 0.508772 0.831325
68 AD9 0.504348 0.811765
69 V2G 0.504274 0.858824
70 A1R 0.504132 0.847059
71 9SN 0.504 0.795455
72 B5Y 0.5 0.813953
73 3OD 0.5 0.833333
74 ABM 0.5 0.788235
75 TYM 0.5 0.86747
76 45A 0.5 0.788235
77 B5M 0.5 0.813953
78 JNT 0.5 0.833333
79 FA5 0.5 0.86747
80 4UU 0.496124 0.813953
81 9X8 0.495935 0.835294
82 5SV 0.495868 0.816092
83 GAP 0.495726 0.811765
84 ACQ 0.495726 0.833333
85 AMP MG 0.495413 0.795181
86 44O 0.492857 0.8125
87 NAI 0.492424 0.784091
88 4UV 0.492188 0.813953
89 HQG 0.491667 0.843373
90 AU1 0.491228 0.811765
91 A12 0.491071 0.845238
92 AP2 0.491071 0.845238
93 44K 0.489051 0.76087
94 A22 0.487603 0.821429
95 D4F 0.485915 0.850575
96 YLB 0.485075 0.873563
97 YLP 0.484848 0.873563
98 XAH 0.484375 0.850575
99 6YZ 0.483333 0.833333
100 ADP MG 0.482456 0.807229
101 ADP BEF 0.482456 0.807229
102 SRA 0.481818 0.833333
103 4UW 0.481203 0.786517
104 DND 0.481203 0.823529
105 NAX 0.481203 0.818182
106 YLY 0.478873 0.863636
107 FYA 0.47619 0.843373
108 MAP 0.47541 0.793103
109 COD 0.47482 0.844444
110 YLC 0.474074 0.872093
111 48N 0.473684 0.816092
112 OZV 0.471545 0.831325
113 9ZA 0.471545 0.825581
114 9ZD 0.471545 0.825581
115 25A 0.471545 0.831325
116 AYB 0.471014 0.863636
117 TAT 0.470588 0.845238
118 T99 0.470588 0.845238
119 APC 0.470085 0.845238
120 DQV 0.469697 0.821429
121 ADQ 0.467742 0.811765
122 TXE 0.466667 0.804598
123 44R 0.466667 0.776596
124 APC MG 0.466102 0.809524
125 ADV 0.466102 0.845238
126 RBY 0.466102 0.845238
127 G3A 0.465649 0.795455
128 KMQ 0.465116 0.802326
129 T5A 0.463768 0.831461
130 YLA 0.463768 0.873563
131 DAL AMP 0.463415 0.821429
132 ANP MG 0.46281 0.8
133 7MD 0.462121 0.872093
134 G5P 0.462121 0.795455
135 CNA 0.460432 0.823529
136 TXD 0.459259 0.804598
137 6V0 0.459259 0.775281
138 GTA 0.458647 0.769231
139 F2R 0.457143 0.852273
140 NAD 0.453901 0.821429
141 ATP MG 0.453782 0.807229
142 ADP PO3 0.453782 0.807229
143 AP0 0.452555 0.755556
144 L3W 0.452555 0.802326
145 AFH 0.451128 0.786517
146 GA7 0.451128 0.781609
147 DZD 0.450704 0.827586
148 BEF ADP 0.45 0.788235
149 25L 0.449612 0.821429
150 A4P 0.449275 0.755319
151 H1Q 0.449153 0.776471
152 N0B 0.44898 0.873563
153 A3D 0.447552 0.811765
154 AMP DBH 0.44697 0.770115
155 ADJ 0.442857 0.820225
156 139 0.442857 0.83908
157 7MC 0.442029 0.852273
158 BQX 0.441176 0.72043
159 ARG AMP 0.440298 0.840909
160 VO4 ADP 0.439024 0.811765
161 ALF ADP 0.439024 0.752809
162 UP5 0.437956 0.813953
163 TAD 0.437037 0.870588
164 LMS 0.433628 0.73913
165 NAD IBO 0.431655 0.809524
166 UPA 0.431655 0.804598
167 NAD TDB 0.431655 0.809524
168 4TC 0.431655 0.816092
169 JB6 0.430769 0.869048
170 8X1 0.428571 0.75
171 M24 0.428571 0.777778
172 TSB 0.428571 0.734043
173 80F 0.427586 0.831461
174 G5A 0.42623 0.755319
175 AOC 0.426087 0.705882
176 SSA 0.424 0.755319
177 5AS 0.423729 0.71875
178 P5A 0.423077 0.797872
179 NAQ 0.422819 0.775281
180 9JJ 0.421687 0.75
181 52H 0.420635 0.71875
182 54H 0.420635 0.726316
183 VMS 0.420635 0.726316
184 53H 0.417323 0.71875
185 A5A 0.416 0.741935
186 ADP BMA 0.415385 0.790698
187 EAD 0.414474 0.777778
188 649 0.414286 0.797872
189 AF3 ADP 3PG 0.414286 0.786517
190 ALF ADP 3PG 0.414286 0.786517
191 0WD 0.413793 0.795455
192 AMP NAD 0.413793 0.821429
193 AHZ 0.413043 0.829545
194 P1H 0.412903 0.78022
195 NDE 0.412903 0.823529
196 DSZ 0.410853 0.774194
197 ATP A A A 0.410448 0.797619
198 8PZ 0.410448 0.755319
199 ATP A 0.410448 0.797619
200 2A5 0.409836 0.833333
201 NDC 0.407643 0.858824
202 YSA 0.407407 0.755319
203 GJV 0.40678 0.727273
204 NAE 0.406667 0.793103
205 PAP 0.406504 0.819277
206 5CA 0.40625 0.755319
207 6RE 0.405172 0.715909
208 NA7 0.40458 0.86747
209 WSA 0.404255 0.763441
210 4TA 0.40411 0.820225
211 5CD 0.40367 0.690476
212 A4D 0.40367 0.702381
213 A3P 0.403361 0.829268
214 FNK 0.402439 0.778947
215 XYA 0.401869 0.702381
216 RAB 0.401869 0.702381
217 ADN 0.401869 0.702381
218 KAA 0.401515 0.787234
219 GSU 0.401515 0.793478
220 7C5 0.40146 0.747126
221 ZID 0.401316 0.811765
222 NSS 0.4 0.755319
223 3AM 0.4 0.795181
224 LSS 0.4 0.739583
Similar Ligands (3D)
Ligand no: 1; Ligand: BT5; Similar ligands found: 0
No: Ligand Similarity coefficient
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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