Receptor
PDB id Resolution Class Description Source Keywords
3Q2I 1.5 Å EC: 1.-.-.- CRYSTAL STRUCTURE OF THE WLBA DEHYDROGNASE FROM CHROMOBACTRI VIOLACEUM IN COMPLEX WITH NADH AND UDP-GLCNACA AT 1.50 A RE CHROMOBACTERIUM VIOLACEUM ROSSMANN FOLD DEHYDROGENASE UDP-SUGAR BINDING NAD BINDINGOXIDOREDUCTASE
Ref.: BIOCHEMICAL AND STRUCTURAL CHARACTERIZATION OF WLBA BORDETELLA PERTUSSIS AND CHROMOBACTERIUM VIOLACEUM: REQUIRED FOR THE BIOSYNTHESIS OF 2,3-DIACETAMIDO-2,3-DIDEOXY-D-MANNURONIC ACID. BIOCHEMISTRY V. 50 1483 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:352;
Invalid;
none;
submit data
35.453 Cl [Cl-]
HP7 A:550;
Valid;
none;
submit data
621.337 C17 H25 N3 O18 P2 CC(=O...
NA A:353;
Part of Protein;
none;
submit data
22.99 Na [Na+]
NAD A:500;
Valid;
none;
submit data
663.425 C21 H27 N7 O14 P2 c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3Q2I 1.5 Å EC: 1.-.-.- CRYSTAL STRUCTURE OF THE WLBA DEHYDROGNASE FROM CHROMOBACTRI VIOLACEUM IN COMPLEX WITH NADH AND UDP-GLCNACA AT 1.50 A RE CHROMOBACTERIUM VIOLACEUM ROSSMANN FOLD DEHYDROGENASE UDP-SUGAR BINDING NAD BINDINGOXIDOREDUCTASE
Ref.: BIOCHEMICAL AND STRUCTURAL CHARACTERIZATION OF WLBA BORDETELLA PERTUSSIS AND CHROMOBACTERIUM VIOLACEUM: REQUIRED FOR THE BIOSYNTHESIS OF 2,3-DIACETAMIDO-2,3-DIDEOXY-D-MANNURONIC ACID. BIOCHEMISTRY V. 50 1483 2011
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 280 families.
1 3Q2I - HP7 C17 H25 N3 O18 P2 CC(=O)N[C@....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 247 families.
1 3Q2K - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
2 3Q2I - HP7 C17 H25 N3 O18 P2 CC(=O)N[C@....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 177 families.
1 3Q2K - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
2 3Q2I - HP7 C17 H25 N3 O18 P2 CC(=O)N[C@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: HP7; Similar ligands found: 66
No: Ligand ECFP6 Tc MDL keys Tc
1 HP7 1 1
2 MJZ 0.824742 0.971014
3 UD1 0.793814 0.985294
4 UD2 0.793814 0.985294
5 UGA 0.776596 0.985075
6 UGB 0.776596 0.985075
7 UD4 0.745098 0.971014
8 UDZ 0.733333 0.905405
9 UD7 0.708738 0.985294
10 EEB 0.697248 0.957143
11 EPZ 0.688073 0.971014
12 EPU 0.681818 0.957143
13 UPG 0.636364 0.970588
14 GDU 0.636364 0.970588
15 UFM 0.636364 0.970588
16 GUD 0.636364 0.970588
17 UMA 0.635593 0.971014
18 HWU 0.633027 0.929577
19 12V 0.633027 0.929577
20 UDM 0.622642 0.942857
21 UAD 0.617647 0.970588
22 UDX 0.617647 0.970588
23 UD0 0.615385 0.87013
24 USQ 0.605769 0.846154
25 UNP 0.604167 0.914286
26 UPF 0.601942 0.916667
27 U2F 0.601942 0.916667
28 UFG 0.601942 0.916667
29 U20 0.592 0.858974
30 U22 0.592 0.8375
31 U21 0.592 0.858974
32 UDP 0.591398 0.941176
33 UTP 0.589474 0.941176
34 G3N 0.584906 0.942857
35 4RA 0.575758 0.881579
36 URM 0.572816 0.928571
37 660 0.572816 0.928571
38 UAG 0.571429 0.917808
39 3UC 0.550459 0.916667
40 IUG 0.538462 0.835443
41 UDH 0.533333 0.842105
42 UPP 0.533333 0.942029
43 UPU 0.529412 0.941176
44 U5P 0.526882 0.926471
45 UML 0.524138 0.858974
46 44P 0.510417 0.901408
47 2KH 0.504951 0.914286
48 UDP UDP 0.494949 0.911765
49 2QR 0.477941 0.848101
50 UDP GAL 0.473214 0.942029
51 Y6W 0.468468 0.890411
52 PMP UD1 0.464286 0.844156
53 UP5 0.456 0.855263
54 C5G 0.443478 0.916667
55 U U 0.438596 0.927536
56 4TC 0.4375 0.833333
57 UUA 0.430108 0.776119
58 URI 0.419355 0.838235
59 U 0.419355 0.838235
60 CXY 0.415254 0.916667
61 2GW 0.414634 0.929577
62 1GW 0.414062 0.891892
63 UAG API 0.411392 0.868421
64 CSQ 0.409836 0.853333
65 CSV 0.409836 0.853333
66 CJB 0.40625 0.823529
Ligand no: 2; Ligand: NAD; Similar ligands found: 220
No: Ligand ECFP6 Tc MDL keys Tc
1 A3D 0.872727 0.986111
2 NAD IBO 0.845455 0.933333
3 NHD 0.821429 0.972222
4 NAP 0.811966 0.986111
5 NAJ PYZ 0.803419 0.910256
6 NFD 0.791304 0.946667
7 NXX 0.765766 0.972603
8 DND 0.765766 0.972603
9 ZID 0.737705 0.986111
10 NAQ 0.729508 0.934211
11 NAE 0.721311 0.959459
12 NA0 0.712 0.972603
13 TAP 0.704 0.921053
14 AMP NAD 0.696 0.945946
15 NDE 0.689922 0.972603
16 NAJ 0.683333 0.972222
17 NDC 0.679389 0.934211
18 NDO 0.674603 0.958904
19 N01 0.656 0.972222
20 CNA 0.642276 0.972603
21 NBP 0.621212 0.922078
22 NAD BBN 0.609929 0.876543
23 8ID 0.609756 0.922078
24 NAD CJ3 0.601399 0.845238
25 ADP MG 0.579439 0.918919
26 A2D 0.576923 0.958333
27 ADP 0.575472 0.931507
28 NGD 0.574803 0.922078
29 BEF ADP 0.574074 0.894737
30 ADP BEF 0.574074 0.894737
31 BA3 0.566038 0.958333
32 NAD NDT 0.565789 0.755319
33 M33 0.564815 0.918919
34 ADP PO3 0.563636 0.957747
35 B4P 0.560748 0.958333
36 AP5 0.560748 0.958333
37 ATP MG 0.558559 0.918919
38 AN2 0.555556 0.918919
39 GAP 0.553571 0.932432
40 OOB 0.551724 0.972222
41 CA0 0.550459 0.932432
42 ATP 0.545455 0.931507
43 ACP 0.545455 0.906667
44 NAD TDB 0.544872 0.70297
45 ADP ALF 0.54386 0.883117
46 ALF ADP 0.54386 0.883117
47 5FA 0.540541 0.931507
48 AQP 0.540541 0.931507
49 APR 0.540541 0.931507
50 AR6 0.540541 0.931507
51 ANP MG 0.53913 0.907895
52 VO4 ADP 0.53913 0.945205
53 ADP VO4 0.53913 0.945205
54 AGS 0.535714 0.883117
55 SAP 0.535714 0.883117
56 AD9 0.535714 0.906667
57 WAQ 0.533333 0.896104
58 ABM 0.53271 0.905405
59 00A 0.529412 0.921053
60 DLL 0.529412 0.972222
61 ANP 0.526316 0.906667
62 NJP 0.526316 0.959459
63 ACQ 0.526316 0.906667
64 OAD 0.525 0.932432
65 AMP MG 0.523364 0.905405
66 ADX 0.522523 0.839506
67 5AL 0.521739 0.945205
68 A1R 0.521008 0.871795
69 9SN 0.520325 0.909091
70 AMP 0.518868 0.930556
71 A 0.518868 0.930556
72 50T 0.517857 0.893333
73 ATF 0.517241 0.894737
74 DAL AMP 0.516949 0.945205
75 3OD 0.516393 0.932432
76 1ZZ 0.516393 0.851852
77 SON 0.513514 0.92
78 PRX 0.513274 0.881579
79 SRP 0.512821 0.92
80 ADP BMA 0.512397 0.932432
81 3UK 0.512397 0.958904
82 MYR AMP 0.512195 0.851852
83 NAJ PZO 0.510949 0.909091
84 NMN 0.509434 0.875
85 AMP DBH 0.507937 0.906667
86 A22 0.504202 0.945205
87 FA5 0.504 0.945946
88 ATP A A A 0.504 0.971831
89 TYR AMP 0.5 0.945946
90 8QN 0.5 0.945205
91 NAX 0.496183 0.886076
92 PR8 0.495935 0.8625
93 PAJ 0.495868 0.873418
94 4AD 0.495868 0.933333
95 AMO 0.495868 0.92
96 ADQ 0.495868 0.932432
97 A12 0.495495 0.894737
98 AP2 0.495495 0.894737
99 ALF ADP 3PG 0.492424 0.873418
100 LA8 ALF 3PG 0.492424 0.873418
101 AHZ 0.492308 0.851852
102 YAP 0.492063 0.933333
103 FYA 0.491935 0.918919
104 AHX 0.491803 0.884615
105 4UU 0.488372 0.933333
106 5SV 0.487603 0.8375
107 TAT 0.487179 0.894737
108 APC 0.486957 0.894737
109 SRA 0.486239 0.881579
110 NAI 0.484848 0.921053
111 6V0 0.484848 0.909091
112 GTA 0.484615 0.898734
113 A A 0.483871 0.958333
114 LAD 0.483871 0.873418
115 AU1 0.482456 0.906667
116 TXE 0.481203 0.921053
117 AF3 ADP 3PG 0.481203 0.873418
118 OMR 0.481203 0.841463
119 LAQ 0.480916 0.851852
120 G3A 0.48062 0.909091
121 TXA 0.48 0.92
122 NB8 0.48 0.884615
123 ME8 0.48 0.851852
124 BIS 0.48 0.871795
125 PTJ 0.48 0.884615
126 139 0.477941 0.886076
127 LPA AMP 0.477273 0.851852
128 AR6 AR6 0.476923 0.958333
129 G5P 0.476923 0.909091
130 AFH 0.476923 0.873418
131 25L 0.47619 0.945205
132 25A 0.47541 0.958333
133 DZD 0.47482 0.897436
134 TXD 0.473684 0.921053
135 4UV 0.472868 0.933333
136 TYM 0.470149 0.945946
137 ADV 0.470085 0.894737
138 RBY 0.470085 0.894737
139 ARG AMP 0.469697 0.841463
140 4TA 0.467626 0.864198
141 48N 0.466165 0.884615
142 XAH 0.465116 0.851852
143 4UW 0.462687 0.897436
144 M24 0.461538 0.886076
145 IOT 0.459854 0.821429
146 T5A 0.456522 0.853659
147 EAD 0.455782 0.886076
148 MAP 0.455285 0.883117
149 BT5 0.453901 0.821429
150 A4P 0.452555 0.833333
151 UP5 0.451852 0.933333
152 PAP 0.445378 0.917808
153 AP0 0.445255 0.884615
154 4TC 0.445255 0.909091
155 YLP 0.444444 0.831325
156 P1H 0.443709 0.864198
157 AOC 0.442478 0.810811
158 Z5A 0.439189 0.833333
159 2A5 0.436975 0.857143
160 G A A A 0.43662 0.909091
161 COD 0.43662 0.802326
162 ADJ 0.435714 0.841463
163 YLC 0.434783 0.851852
164 YLB 0.434783 0.831325
165 U A G G 0.433566 0.921053
166 ATR 0.433333 0.90411
167 7MD 0.432836 0.851852
168 G5A 0.429752 0.790698
169 PO4 PO4 A A A A PO4 0.429688 0.943662
170 TAD 0.42963 0.873418
171 5AS 0.42735 0.770115
172 BTX 0.426573 0.831325
173 YLA 0.425532 0.831325
174 DSZ 0.425197 0.790698
175 NCN 0.424779 0.805556
176 UPA 0.42446 0.921053
177 VMS 0.424 0.8
178 54H 0.424 0.8
179 N0B 0.422819 0.853659
180 6AD 0.422764 0.85
181 AYB 0.422535 0.821429
182 7D3 0.422414 0.844156
183 YLY 0.421769 0.821429
184 TSB 0.420635 0.809524
185 ODP 0.41958 0.922078
186 AV2 0.419355 0.855263
187 FB0 0.419355 0.775281
188 A5A 0.419355 0.819277
189 NNR 0.419048 0.739726
190 A A A 0.418605 0.918919
191 LEU LMS 0.418605 0.793103
192 649 0.417266 0.775281
193 NMN AMP PO4 0.416667 0.933333
194 SSA 0.416 0.790698
195 P5A 0.415385 0.755556
196 LSS 0.414062 0.772727
197 A2R 0.412698 0.918919
198 52H 0.412698 0.790698
199 JB6 0.412214 0.896104
200 5N5 0.411215 0.783784
201 YSA 0.410448 0.811765
202 5CA 0.409449 0.790698
203 53H 0.409449 0.790698
204 ITT 0.408333 0.878378
205 7D4 0.408333 0.844156
206 NA7 0.407692 0.894737
207 5CD 0.407407 0.794521
208 0WD 0.406897 0.909091
209 A3P 0.40678 0.930556
210 AVV 0.40625 0.860759
211 RAB 0.40566 0.808219
212 ADN 0.40566 0.808219
213 XYA 0.40566 0.808219
214 FDA 0.405063 0.823529
215 GSU 0.40458 0.790698
216 7MC 0.404255 0.831325
217 NSS 0.403101 0.811765
218 6FA 0.402516 0.853659
219 NVA LMS 0.4 0.793103
220 PPS 0.4 0.817073
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3Q2I; Ligand: HP7; Similar sites found: 94
This union binding pocket(no: 1) in the query (biounit: 3q2i.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4PNO U5P 0.000003331 0.57331 None
2 3KPE TM3 0.003844 0.47375 None
3 2Z9V PXM 0.008204 0.44644 0.847458
4 3QVL 5HY 0.0002897 0.40828 1.22449
5 1SAZ ACP 0.00000006931 0.45575 1.5748
6 2YP9 SIA CMO 0.006383 0.42795 1.69492
7 3LTW HLZ 0.04487 0.41954 1.78571
8 3RO7 TDR 0.00002489 0.41418 1.88679
9 1E4I NFG 0.000000003505 0.61486 1.9774
10 5T63 ALA ALA ALA ALA 0.0007913 0.44667 1.9774
11 1BGV GLU 0.0001211 0.42595 1.9774
12 3MMR ABH 0.00001664 0.41019 1.9774
13 2Q1A 2KT 0.001533 0.43605 2.04778
14 3RK0 AMP 0.03207 0.40692 2.1097
15 4HPP GLU 0.00005784 0.44367 2.25989
16 1XX4 BAM 0.03206 0.42024 2.29885
17 1KW6 BPY 0.000001385 0.41817 2.39726
18 1V8K ANP 0.002732 0.40416 2.43902
19 2ET1 GLV 0.00003389 0.44119 2.48756
20 3VOZ 04A 0.0001454 0.49269 2.53968
21 1XP8 AGS 0.0000009238 0.46347 2.54237
22 2IZ1 ATR 0.02345 0.43398 2.54237
23 3HPF GAE 0.0003505 0.42089 2.54237
24 1W31 SHO 0.0000001856 0.45774 2.63158
25 1G6O ADP 0.000001153 0.41442 2.72727
26 5DRN 5CT 0.003807 0.50009 2.77778
27 2ZO9 MLI 0.01996 0.41787 2.91971
28 1FNZ A2G 0.00568 0.415 2.95359
29 3KJQ B94 0.001805 0.46173 3.04878
30 4M7F BM3 0.0002417 0.51905 3.09735
31 4P87 4NP 0.001194 0.42688 3.10734
32 3A1I UNU 0.03241 0.41021 3.10734
33 2Z5Y HRM 0.002999 0.40791 3.10734
34 3NJQ NJQ 0.006726 0.40133 3.10881
35 4BPM GSH 0.0002173 0.45566 3.37079
36 1JQ5 NAD 0.00000001568 0.50093 3.38983
37 2ZWS PLM 0.02104 0.46945 3.38983
38 2P8B NSK 0.0000006112 0.45483 3.38983
39 2NZ2 ASP 0.005517 0.45463 3.38983
40 2PP3 LGT 0.000001024 0.4021 3.38983
41 2W3L DRO 0.01922 0.45625 3.47222
42 4DN8 BMA 0.01234 0.44814 3.84615
43 5DTF 5CT 0.03415 0.439 3.91304
44 3VGL BGC 0.0003738 0.43745 4.04984
45 1FRW GTP 0.0000003739 0.40032 4.12371
46 2GJ3 FAD 0.00003519 0.40087 4.16667
47 1MVQ MMA 0.003386 0.40124 4.23729
48 1FX8 BOG 0.02522 0.40182 4.27046
49 1O51 ADP 0.001382 0.42779 4.38596
50 2WGC SIA GAL BGC 0.04841 0.44707 4.67836
51 2NCD ADP 0.008842 0.44998 4.80226
52 3NOJ PYR 0.001118 0.49064 5.04202
53 1J2Z SOG 0.0001653 0.4076 5.18518
54 3SHR CMP 0.04618 0.40318 5.35117
55 4G1V FAD 0.00002348 0.41472 5.36723
56 1A5Z OXM 0.0001446 0.56437 5.64263
57 1A5Z FBP 0.0008146 0.45393 5.64263
58 1S8F GDP 0.02441 0.40873 5.64972
59 3IJH KO2 0.003917 0.47025 5.75221
60 1RSD PSB 0.00003293 0.43703 5.78512
61 2GN2 C5P 0.0003282 0.47838 5.84795
62 1A8S PPI 0.02208 0.4159 5.86081
63 3P7I P7I 0.04884 0.4093 6.23053
64 4HE2 AMP 0.002419 0.40583 6.49718
65 4TMK T5A 0.0000002573 0.4651 6.57277
66 1GXU 2HP 0.00003163 0.49836 6.59341
67 4NTX AMR 0.04695 0.41211 6.66667
68 3FN0 TRP ASN TRP PHE ASP ILE THR ASN LYS 0.006215 0.46321 6.92641
69 3QDY CBS 0.008866 0.46139 6.99301
70 1Y0L HAN 0.001823 0.52332 7.07965
71 43CA NPO 0.04332 0.45007 7.07965
72 5D6C 57S 0.0005099 0.54993 7.14286
73 3DUR KDO 0.04001 0.41763 7.14286
74 3V91 UPG 0.00001834 0.4235 7.2165
75 1F7K UMP 0.01019 0.40149 7.35294
76 1SS4 CIT 0.01792 0.47895 7.84314
77 1NU4 MLA 0.01821 0.46494 8.24742
78 2HVK TBA 0.00485 0.46865 8.6758
79 2BMK PDD 0.01565 0.44562 8.92019
80 3AIQ HBO 0.0001703 0.40728 9.03955
81 3S9K CIT 0.04344 0.43186 9.32203
82 1WKL ADP 0.0000001772 0.49227 10.219
83 1DXY COI 0.04409 0.43577 10.5105
84 3TKA CTN 0.006711 0.5151 10.6628
85 1VQ2 DDN 0.000002478 0.41331 11.9171
86 2PN6 GLN 0.0000002428 0.44095 12
87 1JN2 SFP 0.0002707 0.49209 12.6582
88 1Y2W NAG 0.04494 0.41951 12.6761
89 1TV5 ORO 0.01714 0.41028 12.9944
90 3BY8 MLT 0.04422 0.42466 13.3803
91 4F4S EFO 0.03955 0.41374 18.4211
92 3CH5 GDP 0.003632 0.44846 19.2308
93 4G4S LDZ 0.02623 0.40111 21.8884
94 1UGX GAL MGC 0.002874 0.40852 23.3083
Feedback