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(...
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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: 196
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
7 594 0.583333 0.822917
8 CA0 0.574074 0.833333
9 44L 0.568182 0.793814
10 DLL 0.564103 0.843373
11 A2D 0.556604 0.809524
12 TXA 0.55 0.823529
13 590 0.55 0.833333
14 OOB 0.547009 0.843373
15 5AL 0.54386 0.843373
16 44Q 0.541353 0.836957
17 50T 0.540541 0.8
18 00A 0.537815 0.804598
19 44M 0.535714 0.793814
20 ANP 0.535088 0.811765
21 SRP 0.534483 0.86747
22 8QN 0.533898 0.843373
23 MYR AMP 0.532787 0.829545
24 BA3 0.53211 0.809524
25 LPA AMP 0.53125 0.894118
26 AMO 0.529412 0.86747
27 PAJ 0.529412 0.786517
28 PR8 0.528926 0.904762
29 AP5 0.527273 0.809524
30 ADP 0.527273 0.831325
31 B4P 0.527273 0.809524
32 NB8 0.52459 0.837209
33 OMR 0.523077 0.840909
34 AN2 0.522523 0.821429
35 AR6 0.522124 0.831325
36 APR 0.522124 0.831325
37 3UK 0.520661 0.833333
38 OAD 0.520661 0.833333
39 44N 0.517986 0.842105
40 ADX 0.517857 0.758242
41 M33 0.517857 0.8
42 SAP 0.517544 0.835294
43 AGS 0.517544 0.835294
44 4AD 0.516667 0.857143
45 LAD 0.516393 0.892857
46 AMP 0.514019 0.829268
47 A 0.514019 0.829268
48 ACP 0.513274 0.833333
49 ATP 0.513274 0.831325
50 ATF 0.512821 0.802326
51 AHX 0.512397 0.816092
52 PTJ 0.512195 0.816092
53 BIS 0.512195 0.825581
54 ME8 0.512195 0.850575
55 YAP 0.512 0.857143
56 IOT 0.511278 0.885057
57 SON 0.508929 0.890244
58 PRX 0.508772 0.811765
59 5FA 0.508772 0.831325
60 AQP 0.508772 0.831325
61 AD9 0.504348 0.811765
62 A1R 0.504132 0.847059
63 9SN 0.504 0.795455
64 ABM 0.5 0.788235
65 3OD 0.5 0.833333
66 TYM 0.5 0.86747
67 FA5 0.5 0.86747
68 4UU 0.496124 0.813953
69 5SV 0.495868 0.816092
70 GAP 0.495726 0.811765
71 ACQ 0.495726 0.833333
72 44O 0.492857 0.8125
73 NAI 0.492424 0.784091
74 4UV 0.492188 0.813953
75 AU1 0.491228 0.811765
76 AP2 0.491071 0.845238
77 A12 0.491071 0.845238
78 AMP MG 0.490909 0.767442
79 44K 0.489051 0.76087
80 A22 0.487603 0.821429
81 YLB 0.485075 0.873563
82 YLP 0.484848 0.873563
83 XAH 0.484375 0.850575
84 SRA 0.481818 0.833333
85 NXX 0.481203 0.823529
86 NAX 0.481203 0.818182
87 DND 0.481203 0.823529
88 4UW 0.481203 0.786517
89 YLY 0.478873 0.863636
90 ADP MG 0.478261 0.77907
91 FYA 0.47619 0.843373
92 MAP 0.47541 0.793103
93 COD 0.47482 0.844444
94 ADP BEF 0.474138 0.761364
95 BEF ADP 0.474138 0.761364
96 YLC 0.474074 0.872093
97 48N 0.473684 0.816092
98 25A 0.471545 0.831325
99 AYB 0.471014 0.863636
100 TAT 0.470588 0.845238
101 APC 0.470085 0.845238
102 ADQ 0.467742 0.811765
103 44R 0.466667 0.776596
104 TXE 0.466667 0.804598
105 RBY 0.466102 0.845238
106 ADV 0.466102 0.845238
107 G3A 0.465649 0.795455
108 T5A 0.463768 0.831461
109 YLA 0.463768 0.873563
110 DAL AMP 0.463415 0.821429
111 7MD 0.462121 0.872093
112 G5P 0.462121 0.795455
113 CNA 0.460432 0.823529
114 TXD 0.459259 0.804598
115 6V0 0.459259 0.775281
116 ANP MG 0.459016 0.772727
117 GTA 0.458647 0.769231
118 NAD 0.453901 0.821429
119 ADP PO3 0.453782 0.807229
120 AP0 0.452555 0.755556
121 AFH 0.451128 0.786517
122 DZD 0.450704 0.827586
123 TYR AMP 0.450382 0.823529
124 ATP MG 0.45 0.77907
125 25L 0.449612 0.821429
126 A4P 0.449275 0.755319
127 N0B 0.44898 0.873563
128 A3D 0.447552 0.811765
129 ADP VO4 0.447154 0.8
130 VO4 ADP 0.447154 0.8
131 AMP DBH 0.44697 0.770115
132 139 0.442857 0.83908
133 ADJ 0.442857 0.820225
134 7MC 0.442029 0.852273
135 ADP ALF 0.439024 0.752809
136 ALF ADP 0.439024 0.752809
137 UP5 0.437956 0.813953
138 TAD 0.437037 0.870588
139 ARG AMP 0.433824 0.840909
140 UPA 0.431655 0.804598
141 4TC 0.431655 0.816092
142 JB6 0.430769 0.869048
143 M24 0.428571 0.777778
144 TSB 0.428571 0.734043
145 G5A 0.42623 0.755319
146 AOC 0.426087 0.705882
147 SSA 0.424 0.755319
148 5AS 0.423729 0.71875
149 P5A 0.423077 0.797872
150 A A 0.423077 0.809524
151 NAQ 0.422819 0.775281
152 VMS 0.420635 0.726316
153 54H 0.420635 0.726316
154 52H 0.420635 0.71875
155 53H 0.417323 0.71875
156 NAD IBO 0.416667 0.772727
157 A5A 0.416 0.741935
158 ADP BMA 0.415385 0.790698
159 EAD 0.414474 0.777778
160 ALF ADP 3PG 0.414286 0.786517
161 AF3 ADP 3PG 0.414286 0.786517
162 LA8 ALF 3PG 0.414286 0.786517
163 649 0.414286 0.797872
164 0WD 0.413793 0.795455
165 AHZ 0.413043 0.829545
166 NDE 0.412903 0.823529
167 P1H 0.412903 0.78022
168 DSZ 0.410853 0.774194
169 AMP NAD 0.410596 0.802326
170 ATP A A A 0.410448 0.797619
171 2A5 0.409836 0.833333
172 NDC 0.407643 0.858824
173 YSA 0.407407 0.755319
174 GJV 0.40678 0.727273
175 NAE 0.406667 0.793103
176 PAP 0.406504 0.819277
177 5CA 0.40625 0.755319
178 6RE 0.405172 0.715909
179 NA7 0.40458 0.86747
180 WSA 0.404255 0.763441
181 4TA 0.40411 0.820225
182 NAJ PYZ 0.403974 0.758242
183 A4D 0.40367 0.702381
184 5CD 0.40367 0.690476
185 A3P 0.403361 0.829268
186 FNK 0.402439 0.778947
187 XYA 0.401869 0.702381
188 ADN 0.401869 0.702381
189 RAB 0.401869 0.702381
190 KAA 0.401515 0.787234
191 GSU 0.401515 0.793478
192 7C5 0.40146 0.747126
193 ZID 0.401316 0.811765
194 NSS 0.4 0.755319
195 3AM 0.4 0.795181
196 LSS 0.4 0.739583
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2DXU; Ligand: BT5; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2DXU; Ligand: BT5; Similar sites found: 30
This union binding pocket(no: 2) in the query (biounit: 2dxu.bio1) has 34 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2GUC MAN 0.005661 0.429 None
2 3B6R ADP 0.006406 0.42594 2.12766
3 4L50 D8X 0.01912 0.41027 2.55319
4 1WD4 AHR 0.005503 0.44625 2.97872
5 2GN3 MAN 0.006384 0.42991 3.40426
6 2GN3 MMA 0.007103 0.42782 3.40426
7 1J71 THR ILE THR SER 0.02594 0.4166 3.40426
8 4CS4 AXZ 0.003395 0.41235 3.40426
9 4CS4 ANP 0.003754 0.40453 3.40426
10 2WKQ FMN 0.006139 0.41963 4.25532
11 1N9L FMN 0.005616 0.42139 5.50459
12 3ZJX BOG 0.04119 0.40134 5.53191
13 2RCU BUJ 0.00729 0.40604 5.95745
14 2V0U FMN 0.005659 0.42124 6.16438
15 3A7R LAQ 0.0001229 0.45855 6.38298
16 4H2X G5A 0.01379 0.40363 6.80851
17 2E5A LAQ 0.0003815 0.42496 7.23404
18 4LO2 GAL BGC 0.009415 0.44985 7.48299
19 1DZK PRZ 0.00781 0.42185 8.28025
20 2IU8 PLM 0.00311 0.42601 9.3617
21 3DLG GWE 0.01289 0.40097 9.3617
22 5EW9 5VC 0.02332 0.40604 9.78723
23 1V6A TRE 0.0264 0.41587 11.4894
24 2QHV OC9 0.002373 0.46522 11.9048
25 3EB9 FLC 0.02921 0.40106 14.0426
26 5L2J 6UL 0.002126 0.43437 19.1489
27 5L2J 70E 0.002298 0.43437 19.1489
28 4Q3F TLA 0.02551 0.4228 22.2222
29 2ART LPA AMP 0.00005066 0.4457 22.5532
30 2CJU PHX 0.01231 0.43203 23.8938
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