Receptor
PDB id Resolution Class Description Source Keywords
1YBQ 2 Å EC: 3.4.19.- CRYSTAL STRUCTURE OF ESCHERICHIA COLI ISOASPARTYL DIPEPTIDAS D285N COMPLEXED WITH BETA-ASPARTYLHISTIDINE ESCHERICHIA COLI HYDROLASE DIPEPTIDASE
Ref.: MECHANISM OF THE REACTION CATALYZED BY ISOASPARTYL DIPEPTIDASE FROM ESCHERICHIA COLI. BIOCHEMISTRY V. 44 7115 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BDH A:393;
B:393;
Valid;
Valid;
none;
none;
submit data
270.242 C10 H14 N4 O5 c1c([...
ZN A:391;
A:392;
B:391;
B:392;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1YBQ 2 Å EC: 3.4.19.- CRYSTAL STRUCTURE OF ESCHERICHIA COLI ISOASPARTYL DIPEPTIDAS D285N COMPLEXED WITH BETA-ASPARTYLHISTIDINE ESCHERICHIA COLI HYDROLASE DIPEPTIDASE
Ref.: MECHANISM OF THE REACTION CATALYZED BY ISOASPARTYL DIPEPTIDASE FROM ESCHERICHIA COLI. BIOCHEMISTRY V. 44 7115 2005
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1YBQ - BDH C10 H14 N4 O5 c1c([nH]cn....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1YBQ - BDH C10 H14 N4 O5 c1c([nH]cn....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1YBQ - BDH C10 H14 N4 O5 c1c([nH]cn....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: BDH; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 BDH 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1YBQ; Ligand: BDH; Similar sites found: 222
This union binding pocket(no: 1) in the query (biounit: 1ybq.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2E1A MSE 0.0151 0.40989 None
2 2YIP YIO 0.009671 0.41038 1.44928
3 1G41 ADP 0.00009688 0.4318 1.53846
4 4QN6 LNV 0.00007431 0.417 1.53846
5 2NLI LAC 0.000006821 0.46023 1.63043
6 2NLI FMN 0.000006821 0.46023 1.63043
7 2Q6K ADN 0.001935 0.40533 1.76678
8 4KS1 2H8 0.0001053 0.4204 1.79487
9 1QW9 KHP 0.00001418 0.41121 1.79487
10 2BGM NAJ 0.00004545 0.44309 1.79856
11 3EAU PDN 0.0001514 0.44193 1.83486
12 3EAU NDP 0.0001514 0.44193 1.83486
13 3FPZ AHZ 0.0000221 0.46727 1.84049
14 1YOE RIB 0.00001347 0.41963 1.86335
15 4IVG ANP 0.000001095 0.48253 2.05128
16 1ZFJ IMP 0.0001079 0.45514 2.05128
17 4KCF FMN 0.00000332 0.45275 2.05128
18 2YYJ FAD 0.0005467 0.42626 2.05128
19 2YYJ 4HP 0.0005467 0.42626 2.05128
20 1VCO GLN 0.000005498 0.4258 2.05128
21 4KCF AKM 0.0004612 0.40887 2.05128
22 4MWV BCZ 0.0000824 0.41581 2.06186
23 1GR0 NAD 0.00006975 0.44927 2.17984
24 2ZO9 MLI 0.0002307 0.47884 2.18978
25 3OIG NAD 0.000007859 0.46698 2.25564
26 3OIG IMJ 0.0001647 0.40111 2.25564
27 1I2B NAD 0.0002362 0.45444 2.30769
28 1I2B USQ 0.0002362 0.45444 2.30769
29 1I2B UPG 0.0002362 0.45444 2.30769
30 4Q0P 0MK 0.0005279 0.43248 2.30769
31 1WL4 COA 0.0000466 0.43008 2.30769
32 2R0N FAD 0.0004798 0.42798 2.30769
33 2R0N TGC 0.006977 0.4066 2.30769
34 1JCM 137 0.00002389 0.41371 2.3166
35 2TOH HBI 0.000006894 0.41604 2.33236
36 2P2V CSF 0.000003407 0.46869 2.43056
37 2IMP NAI 0.0004615 0.42725 2.5641
38 2GGH NLQ 0.000009453 0.43766 2.66667
39 2ZI8 SDT 0.00007668 0.40142 2.66667
40 1JQN DCO 0.000001982 0.46337 2.71801
41 1OMZ UD2 0.0000634 0.42643 2.73038
42 2WSB NAD 0.02797 0.40771 2.75591
43 2Q37 3AL 0.01426 0.42021 2.76243
44 4PVV HO4 0.03021 0.40421 2.77778
45 3VGL ANP 0.00002891 0.42786 2.82051
46 4GZP G39 0.0002063 0.40776 2.82051
47 1G6O ADP 0.0002283 0.42119 3.0303
48 4G1V FAD 0.000244 0.44349 3.07692
49 3PLN U5P 0.003666 0.44175 3.07692
50 3D2M COA 0.001287 0.42242 3.07692
51 2Z5Y HRM 0.0002696 0.41744 3.07692
52 3DJL FAD 0.001045 0.41649 3.07692
53 3O03 NAP 0.00006774 0.43811 3.09278
54 4CMF PXG 0.00000258 0.47208 3.10559
55 3VZS NAP 0.03358 0.40706 3.11284
56 4IZC 1GZ 0.0002015 0.41847 3.27273
57 1K97 CIR 0.0001118 0.44727 3.33333
58 1K97 ASP 0.0001118 0.44727 3.33333
59 1Y42 TYR 0.009526 0.42326 3.33333
60 2RGO FAD 0.02337 0.40883 3.33333
61 3K37 BCZ 0.002664 0.40298 3.33333
62 2Z9V PXM 0.02969 0.40112 3.33333
63 2RDT 2RD 0.0000004794 0.50841 3.35917
64 2RDT FMN 0.000000199 0.50841 3.35917
65 4TSK NDP 0.00009841 0.43345 3.42857
66 1A5Z NAD 0.00004578 0.43488 3.44828
67 2X61 NGA GAL SIA 0.000001114 0.48934 3.48837
68 2X61 CH 0.0000002278 0.48695 3.48837
69 2BLE 5GP 0.000004271 0.47464 3.54223
70 1Q3Q ANP 0.00003805 0.44531 3.58974
71 2PP3 LGT 0.00004374 0.41341 3.58974
72 4HZX G39 0.0003566 0.40139 3.60825
73 1P4C FMN 0.00000154 0.49347 3.68421
74 3C2O NTM 0.00005556 0.46175 3.7415
75 2RHQ GAX 0.0006135 0.42716 3.7415
76 1UGX GAL MGC 0.000973 0.40088 3.7594
77 1GSA GSH 0.00004441 0.4282 3.79747
78 1GSA ADP 0.0001078 0.42453 3.79747
79 3F81 STT 0.02949 0.42092 3.82514
80 1SAY PYR 0.0005438 0.44135 3.84615
81 1BGV GLU 0.00005556 0.4074 3.84615
82 3C3N FMN 0.02778 0.4031 3.84615
83 4G87 UD1 0.0007201 0.40011 3.84615
84 1OVD ORO 0.03322 0.40023 3.85852
85 4F4S EFO 0.01517 0.41422 3.94737
86 3P3N AKG 0.00552 0.44503 4.01146
87 2IYG FMN 0.01571 0.40115 4.03226
88 1EDO NAP 0.00002346 0.46026 4.09836
89 2F2U M77 0.01868 0.40185 4.10256
90 3CXO 1N5 0.0001111 0.40101 4.10256
91 1SJW NGV 0.008486 0.40442 4.16667
92 3UXL CFI 0.00006844 0.45769 4.17755
93 2XD9 XD9 0.00058 0.44586 4.19162
94 3MAG 3MA 0.0482 0.42195 4.23453
95 3WSJ MK1 0.0002658 0.41362 4.31034
96 2QS8 MET 0.0000153 0.41799 4.35897
97 4A3R CIT 0.00005643 0.41734 4.35897
98 1MXI SAH 0.006277 0.40232 4.375
99 2ET1 GLV 0.00006329 0.42019 4.47761
100 1DXY NAD 0.003816 0.40468 4.5045
101 2NCD ADP 0.03142 0.40431 4.52381
102 3RO7 TDR 0.00002577 0.47401 4.5283
103 2BJF DXC 0.000001951 0.43219 4.55927
104 1SS4 GSH 0.001081 0.53247 4.57516
105 1YBH FAD 0.00000951 0.48279 4.61538
106 1YBH P22 0.00001103 0.42514 4.61538
107 1T26 NAI 0.00003591 0.46889 4.65839
108 1T26 GBD 0.00003591 0.46889 4.65839
109 3ZPG 5GP 0.01026 0.4516 4.71204
110 2C1Q BTN 0.00004016 0.4268 4.7619
111 2OWZ F6P 0.00006145 0.42185 4.81928
112 3O9P MHI 0.00173 0.40283 4.87179
113 1WVC CTP 0.00002281 0.46972 5.01931
114 4AF0 IMP 0.000004192 0.46377 5.12821
115 4DA6 GA2 0.001058 0.4022 5.13834
116 1RP0 AHZ 0.000006281 0.47724 5.28169
117 4A8T PAO 0.00003362 0.45054 5.30973
118 3MMR ABH 0.0000433 0.44177 5.38462
119 1N6B DMZ 0.00001102 0.43896 5.38462
120 2C9O ADP 0.0006421 0.41763 5.38462
121 4CCO OGA 0.01379 0.41608 5.38462
122 1CR1 TTP 0.00009936 0.44167 5.40541
123 1NVU GTP 0.00007176 0.43552 5.42169
124 4HE2 AMP 0.0000042 0.43684 5.6213
125 4P87 4NP 0.000008404 0.41785 5.64103
126 4QN7 G39 0.0001422 0.40684 5.64103
127 4EKV BTN 0.000002833 0.44671 5.66038
128 1LGT BP3 0.0004123 0.44657 5.72391
129 3M0J OAF 0.00002359 0.41927 5.86319
130 4B7J G39 0.00002134 0.4237 5.89744
131 3A1I UNU 0.01786 0.40267 5.89744
132 3IU9 T07 0.0003174 0.41969 5.90278
133 1RM4 NDP 0.00008481 0.4371 5.93472
134 1O9U ADZ 0.003162 0.47878 6
135 1AL8 DHP 0.0000868 0.44022 6.12813
136 1AL8 FMN 0.0003011 0.41407 6.12813
137 1X1T NAD 0.000002432 0.49126 6.15385
138 1V8K ANP 0.00002759 0.41442 6.15385
139 1WMA AB3 0.03105 0.40798 6.15942
140 3UC5 ATP 0.00001227 0.46042 6.36943
141 1HV9 UD1 0.0001437 0.4003 6.41026
142 1I9G SAM 0.000008134 0.45333 6.42857
143 3CKZ ZMR 0.00006063 0.42454 6.49351
144 1KW6 BPY 0.0001717 0.42992 6.50685
145 2NSJ C2R 0.0003109 0.4284 6.50888
146 1WKL ATP 0.0002471 0.41744 6.56934
147 4TMK T5A 0.00005851 0.4696 6.57277
148 1NVV GNP 0.0002103 0.4222 6.62651
149 1Z44 FMN 0.01162 0.40272 6.80473
150 3V91 UPG 0.00008581 0.42728 6.87285
151 4F8L GAL 0.02752 0.44354 6.89655
152 1LTH NAD 0.00009961 0.42954 6.89655
153 1YOA FMN 0.04952 0.4285 6.91824
154 1YOA FAD 0.001921 0.4103 6.91824
155 1PJ6 FOL 0.000001408 0.47162 6.92308
156 4OYA 1VE 0.001089 0.4247 6.92308
157 2HMT NAI 0.00007042 0.42967 6.94444
158 4FUA PGH 0.000004751 0.47864 6.97674
159 1LDM NAD 0.0002907 0.42483 6.99088
160 2FH5 GTP 0.00009489 0.42164 7.02703
161 4JP3 CIT 0.000001896 0.45101 7.11297
162 1ME8 RVP 0.00001743 0.47039 7.17949
163 1BDB NAD 0.000005982 0.4796 7.22022
164 1V6A TRE 0.003722 0.44708 7.53012
165 4Q3S X7A 0.0006663 0.41529 7.53247
166 1FWY UD1 0.00004452 0.41249 7.85498
167 1ZK4 NAP 0.000008664 0.4796 7.96813
168 1ZK4 AC0 0.000008664 0.4796 7.96813
169 3HPF GAE 0.00002935 0.42478 8.20513
170 1PEA ACM 0.03623 0.4163 8.31169
171 1TV5 ORO 0.00007791 0.48018 8.46154
172 1TV5 A26 0.0008077 0.4231 8.46154
173 3FSJ D7K 0.0005364 0.41994 8.46154
174 1WDA BAG 0.0102 0.41728 8.46154
175 1TV5 N8E 0.004034 0.40937 8.46154
176 3TA2 AKG 0.00003137 0.40787 8.47458
177 4LCQ URQ 0.00001708 0.41804 8.71795
178 1C1L GAL BGC 0.008431 0.44229 8.75912
179 1JA9 NDP 0.0003023 0.42733 8.75912
180 1JA9 PYQ 0.00002467 0.41349 8.75912
181 3Q3C NAD 0.0001832 0.42205 9.0301
182 3BY8 MLT 0.02435 0.4195 9.15493
183 2O2C G6Q 0.007342 0.40686 9.23077
184 1QCA FUA 0.0002763 0.42625 9.38967
185 2Q1A 2KT 0.0000009404 0.42852 9.55631
186 1F8F NAD 0.000119 0.42925 9.7035
187 1FNZ A2G 0.000009473 0.48879 9.70464
188 2RHW C0E 0.00003487 0.45007 9.89399
189 4P4T GDP 0.005992 0.40306 10.2778
190 3H86 AP5 0.0004642 0.40539 10.4167
191 4N02 FNR 0.000009478 0.45844 10.5128
192 3QVL 5HY 0.00003507 0.44133 10.6122
193 1EXB NDP 0.00001274 0.4698 11.6505
194 2NZ2 CIR 0.00001413 0.41086 11.7949
195 1XP8 AGS 0.0001702 0.41581 12.0219
196 1CFV E3G 0.001459 0.40449 12.3894
197 2P8B NSK 0.0001448 0.45547 12.4661
198 1XMV ADP 0.00033 0.41389 12.6404
199 1DRV A3D 0.0002801 0.41298 12.8205
200 3K9W ADE 0.001004 0.42428 12.8342
201 3K9W 4PS 0.001004 0.42428 12.8342
202 1JQ5 NAD 0.005563 0.41129 12.973
203 1G8S MET 0.004366 0.44987 13.4783
204 3ORF NAD 0.01382 0.41237 13.5458
205 2QLX RM4 0.005729 0.45056 13.8889
206 4LBP 1WG 0.00007064 0.40063 14
207 1RZM E4P 0.005876 0.45002 14.7929
208 1RZM PEP 0.01056 0.42125 14.7929
209 1OFH ADP 0.001116 0.40396 14.9425
210 3DGB MUC 0.012 0.40595 15.1832
211 2WLT ASP 0.000003395 0.47387 15.9639
212 1RSD PSB 0.0007186 0.45061 16.5289
213 2Z9I GLY ALA THR VAL 0.01398 0.40174 17.284
214 1N9L FMN 0.006608 0.4015 17.4312
215 1V5F TPP 0.001282 0.43668 17.6923
216 1V5F FAD 0.001282 0.43668 17.6923
217 4C25 13P 0.00001649 0.40251 17.9245
218 2GJ3 FAD 0.000378 0.42858 20.8333
219 1GXU 2HP 0.001939 0.41015 20.8791
220 3ZZS TRP 0.0001242 0.40838 21.5385
221 3KPE TM3 0.001099 0.47832 25.641
222 4GQB 0XU 0.0000504 0.43791 27.2727
Pocket No.: 2; Query (leader) PDB : 1YBQ; Ligand: BDH; 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: 1ybq.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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