Receptor
PDB id Resolution Class Description Source Keywords
3PLR 1.7 Å EC: 1.1.1.22 CRYSTAL STRUCTURE OF KLEBSIELLA PNEUMONIAE UDP-GLUCOSE 6-DEH COMPLEXED WITH NADH AND UDP-GLUCOSE KLEBSIELLA PNEUMONIAE ROSSMANN FOLD DEHYDROGENASE OXIDOREDUCTASE
Ref.: CONFORMATIONAL CHANGE UPON PRODUCT BINDING TO KLEBS PNEUMONIAE UDP-GLUCOSE DEHYDROGENASE: A POSSIBLE IN MECHANISM FOR THE KEY ENZYME IN POLYMYXIN RESISTANC J.STRUCT.BIOL. V. 175 300 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAI A:900;
 Valid;
 none;
 submit data
665.441 C21 H29 N7 O14 P2 c1nc(...
U5P A:901;
 Valid;
 none;
 submit data
324.181 C9 H13 N2 O9 P C1=CN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3PLN 1.5 Å EC: 1.1.1.22 CRYSTAL STRUCTURE OF KLEBSIELLA PNEUMONIAE UDP-GLUCOSE 6-DEH COMPLEXED WITH UDP-GLUCOSE KLEBSIELLA PNEUMONIAE ROSSMANN FOLD DEHYDROGENASE OXIDOREDUCTASE
Ref.: CONFORMATIONAL CHANGE UPON PRODUCT BINDING TO KLEBS PNEUMONIAE UDP-GLUCOSE DEHYDROGENASE: A POSSIBLE IN MECHANISM FOR THE KEY ENZYME IN POLYMYXIN RESISTANC J.STRUCT.BIOL. V. 175 300 2011
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 3PLR - U5P C9 H13 N2 O9 P C1=CN(C(=O....
2 3PLN - U5P C9 H13 N2 O9 P C1=CN(C(=O....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3PLR - U5P C9 H13 N2 O9 P C1=CN(C(=O....
2 3PLN - U5P C9 H13 N2 O9 P C1=CN(C(=O....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1DLI - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
2 1DLJ - NAI C21 H29 N7 O14 P2 c1nc(c2c(n....
3 3PLR - U5P C9 H13 N2 O9 P C1=CN(C(=O....
4 3PLN - U5P C9 H13 N2 O9 P C1=CN(C(=O....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: NAI; Similar ligands found: 287
No: Ligand ECFP6 Tc MDL keys Tc
1 NAI 1 1
2 0WD 0.814815 0.986842
3 NDP 0.803738 0.986842
4 AP0 0.743119 0.961039
5 NMN AMP PO4 0.704348 0.960526
6 NAX 0.663717 0.961538
7 A2D 0.659574 0.933333
8 80F 0.65 0.925926
9 6V0 0.649123 0.986842
10 TXE 0.62931 0.948052
11 BA3 0.628866 0.933333
12 AP5 0.622449 0.933333
13 B4P 0.622449 0.933333
14 TXD 0.62069 0.923077
15 APR 0.613861 0.907895
16 AR6 0.613861 0.907895
17 EAD 0.609375 0.961538
18 AGS 0.607843 0.8625
19 ADP 0.606061 0.907895
20 50T 0.60396 0.871795
21 ATP 0.60396 0.907895
22 HEJ 0.60396 0.907895
23 AT4 0.6 0.873418
24 AN2 0.6 0.896104
25 A22 0.598131 0.921053
26 5FA 0.598039 0.907895
27 AQP 0.598039 0.907895
28 CA0 0.594059 0.909091
29 M33 0.594059 0.896104
30 AD9 0.592233 0.884615
31 NAJ PZO 0.592 0.935897
32 P1H 0.590909 0.9375
33 ACP 0.588235 0.884615
34 KG4 0.588235 0.909091
35 4AD 0.587156 0.886076
36 A1R 0.587156 0.851852
37 PRX 0.582524 0.8375
38 ANP 0.580952 0.884615
39 3OD 0.580357 0.909091
40 SRP 0.579439 0.873418
41 ADX 0.578431 0.821429
42 OAD 0.576577 0.909091
43 5AL 0.575472 0.896104
44 HQG 0.574074 0.896104
45 NAJ PYZ 0.573643 0.890244
46 A3R 0.572727 0.851852
47 ADJ 0.569106 0.890244
48 8LQ 0.568807 0.873418
49 UP5 0.566667 0.960526
50 ACQ 0.566038 0.884615
51 8LH 0.564815 0.873418
52 9X8 0.5625 0.8625
53 A 0.561224 0.881579
54 AMP 0.561224 0.881579
55 8LE 0.560748 0.8625
56 ATF 0.555556 0.873418
57 QA7 0.554545 0.8625
58 JNT 0.553571 0.884615
59 6YZ 0.550459 0.884615
60 8QN 0.54955 0.896104
61 25L 0.547826 0.921053
62 4TC 0.544715 0.935897
63 AMO 0.544643 0.897436
64 ADQ 0.544643 0.909091
65 PAJ 0.544643 0.853659
66 ABM 0.544554 0.858974
67 45A 0.544554 0.858974
68 NPW 0.544 0.949367
69 LAD 0.54386 0.831325
70 PR8 0.54386 0.821429
71 WAQ 0.54386 0.851852
72 DQV 0.541667 0.946667
73 DG1 0.541353 0.986842
74 1DG 0.541353 0.986842
75 AMP MG 0.54 0.868421
76 00A 0.539823 0.875
77 NZQ 0.539683 0.974026
78 1ZZ 0.53913 0.811765
79 BIS 0.53913 0.851852
80 APC 0.537736 0.873418
81 OMR 0.536585 0.823529
82 25A 0.535714 0.907895
83 5SV 0.535714 0.797619
84 OOB 0.535714 0.921053
85 3UK 0.535088 0.909091
86 A12 0.533981 0.873418
87 AP2 0.533981 0.873418
88 B5V 0.530435 0.897436
89 DND 0.528455 0.922078
90 CNA 0.527559 0.922078
91 AHX 0.526316 0.864198
92 DLL 0.526316 0.921053
93 NB8 0.525862 0.864198
94 ME8 0.525862 0.811765
95 PTJ 0.525862 0.841463
96 FYA 0.525862 0.871795
97 KMQ 0.525424 0.897436
98 B5M 0.525424 0.886076
99 SRA 0.524752 0.8375
100 ADP MG 0.52381 0.881579
101 ADP BEF 0.52381 0.881579
102 SON 0.52381 0.873418
103 TAT 0.522936 0.873418
104 T99 0.522936 0.873418
105 OZV 0.522124 0.907895
106 YLP 0.520325 0.793103
107 48N 0.520325 0.864198
108 L3W 0.52 0.973333
109 YLB 0.52 0.793103
110 AU1 0.518868 0.884615
111 ADP PO3 0.518519 0.881579
112 ATP MG 0.518519 0.881579
113 V2G 0.518182 0.841463
114 9SN 0.516949 0.864198
115 BEF ADP 0.513761 0.858974
116 DAL AMP 0.513274 0.871795
117 TXA 0.512821 0.897436
118 FA5 0.512605 0.897436
119 B5Y 0.512605 0.886076
120 GAP 0.509091 0.860759
121 9ZA 0.508772 0.851852
122 9ZD 0.508772 0.851852
123 4UU 0.508197 0.960526
124 YLC 0.507937 0.833333
125 T5A 0.507812 0.925926
126 RBY 0.504587 0.873418
127 APC MG 0.504587 0.858974
128 ADV 0.504587 0.873418
129 4UW 0.504 0.924051
130 TXP 0.503876 0.911392
131 VO4 ADP 0.5 0.860759
132 LAQ 0.5 0.811765
133 TYM 0.5 0.897436
134 G3A 0.5 0.8875
135 F2R 0.5 0.813953
136 ANP MG 0.5 0.871795
137 ALF ADP 0.5 0.817073
138 COD 0.496183 0.786517
139 YLA 0.496124 0.813953
140 139 0.496124 0.9125
141 AFH 0.495935 0.853659
142 G5P 0.495935 0.8875
143 XAH 0.495868 0.811765
144 BT5 0.492424 0.784091
145 AYB 0.492308 0.784091
146 A4P 0.492188 0.880952
147 GTA 0.491935 0.855422
148 4UV 0.491803 0.960526
149 A2R 0.491228 0.896104
150 MAP 0.486957 0.8625
151 XNP 0.484848 0.936709
152 NAD 0.484848 0.921053
153 UPA 0.484375 0.948052
154 7MD 0.483871 0.833333
155 ARG AMP 0.483871 0.781609
156 MYR AMP 0.483333 0.790698
157 NA7 0.483051 0.873418
158 YLY 0.477941 0.784091
159 ATR 0.477477 0.881579
160 ALF ADP 3PG 0.476562 0.809524
161 AOC 0.47619 0.792208
162 ATP A 0.47541 0.894737
163 ATP A A A 0.47541 0.894737
164 BTX 0.473684 0.793103
165 NDP DTT 0.472222 0.902439
166 5AS 0.472222 0.736264
167 GA7 0.472 0.873418
168 LMS 0.471154 0.77907
169 NAQ 0.471014 0.864198
170 LEU LMS 0.470588 0.709677
171 ADP BMA 0.470588 0.884615
172 N0B 0.467626 0.835294
173 A3D 0.466667 0.909091
174 NJP 0.466165 0.910256
175 IOT 0.465649 0.784091
176 AF3 ADP 3PG 0.465116 0.809524
177 PAP 0.464286 0.894737
178 D4F 0.463768 0.833333
179 NAE 0.463768 0.886076
180 NAD TDB 0.461538 0.907895
181 NAD IBO 0.461538 0.907895
182 7MC 0.461538 0.813953
183 H1Q 0.459459 0.846154
184 DZD 0.459259 0.876543
185 ZID 0.457143 0.909091
186 TAD 0.456693 0.853659
187 2A5 0.455357 0.8375
188 62F 0.453947 0.833333
189 AHZ 0.453125 0.790698
190 FB0 0.452055 0.76087
191 JB6 0.45082 0.851852
192 7D4 0.45045 0.825
193 ITT 0.45045 0.857143
194 LPA AMP 0.449612 0.790698
195 G5A 0.447368 0.755556
196 M24 0.446043 0.843373
197 AVV 0.445378 0.841463
198 NDC 0.442177 0.864198
199 NSS 0.441667 0.775281
200 4TA 0.441176 0.890244
201 54H 0.440678 0.764045
202 VMS 0.440678 0.764045
203 7D3 0.440367 0.825
204 5CD 0.44 0.753247
205 PPS 0.439655 0.8
206 XYA 0.438776 0.789474
207 RAB 0.438776 0.789474
208 ADN 0.438776 0.789474
209 NDE 0.438356 0.897436
210 NVA LMS 0.438017 0.731183
211 AR6 AR6 0.4375 0.883117
212 8X1 0.436975 0.731183
213 TSB 0.436975 0.793103
214 53H 0.436975 0.755556
215 DTA 0.436893 0.759494
216 A3P 0.436364 0.881579
217 A2P 0.436364 0.868421
218 A5A 0.435897 0.781609
219 FNK 0.435065 0.840909
220 HFD 0.434783 0.8625
221 JSQ 0.434783 0.8625
222 ODP 0.433824 0.924051
223 SFG 0.433628 0.725
224 Z5A 0.433566 0.858824
225 6FA 0.433333 0.835294
226 SSA 0.432203 0.775281
227 J7C 0.431193 0.702381
228 DTP 0.431034 0.825
229 P5A 0.430894 0.723404
230 AMP NAD 0.430657 0.896104
231 5N5 0.43 0.766234
232 DSZ 0.429752 0.775281
233 LSS 0.429752 0.73913
234 NO7 0.428571 0.873418
235 52H 0.428571 0.755556
236 SFD 0.427632 0.731959
237 9K8 0.427419 0.712766
238 6AD 0.42735 0.831325
239 EP4 0.427184 0.707317
240 FDA 0.426667 0.870588
241 ARU 0.42623 0.788235
242 6RE 0.425926 0.694118
243 A4D 0.425743 0.766234
244 5CA 0.425 0.775281
245 3DH 0.424528 0.725
246 AV2 0.423729 0.835443
247 AMP DBH 0.421875 0.860759
248 5X8 0.421053 0.7375
249 DAT 0.421053 0.825
250 GSU 0.419355 0.755556
251 MTA 0.419048 0.725
252 3AT 0.418803 0.883117
253 ETB 0.41844 0.786517
254 DCA 0.41844 0.777778
255 FAS 0.418301 0.845238
256 FAD 0.418301 0.845238
257 A3N 0.418182 0.759494
258 K3K 0.417323 0.797468
259 F2N 0.417178 0.850575
260 38V 0.416667 0.855422
261 7D5 0.415094 0.8
262 B1U 0.414062 0.734043
263 YSA 0.414062 0.775281
264 NAD BBN 0.412903 0.835294
265 0T1 0.412587 0.777778
266 2AM 0.411215 0.857143
267 K3E 0.410853 0.7875
268 9JJ 0.409938 0.855422
269 M2T 0.409524 0.690476
270 CUU 0.408696 0.883117
271 V47 0.408333 0.779221
272 KAA 0.408 0.731183
273 7C5 0.407692 0.790123
274 3AM 0.407407 0.844156
275 NAP 0.406897 0.909091
276 8PZ 0.40625 0.795455
277 KOY 0.406015 0.797468
278 PUA 0.405594 0.9
279 FAY 0.405063 0.855422
280 P5F 0.404908 0.83908
281 EEM 0.403361 0.670455
282 COA 0.402778 0.777778
283 RFL 0.402516 0.816092
284 GJV 0.401786 0.686047
285 6MZ 0.401786 0.846154
286 SA8 0.401709 0.686047
287 WSA 0.4 0.784091
Ligand no: 2; Ligand: U5P; Similar ligands found: 125
No: Ligand ECFP6 Tc MDL keys Tc
1 U5P 1 1
2 U 1 1
3 44P 0.790323 0.941176
4 UDP 0.78125 0.984615
5 UTP 0.746269 0.984615
6 2KH 0.735294 0.955224
7 U5F 0.735294 0.984615
8 UDP UDP 0.727273 0.953846
9 UPU 0.694444 0.954545
10 UNP 0.690141 0.955224
11 660 0.662338 0.913043
12 URM 0.662338 0.913043
13 URI 0.661017 0.848485
14 GDU 0.641026 0.926471
15 UFM 0.641026 0.926471
16 UPG 0.641026 0.926471
17 U2F 0.6375 0.875
18 UPF 0.6375 0.875
19 Y6W 0.632911 0.875
20 UDH 0.628205 0.851351
21 UPP 0.628205 0.926471
22 UFG 0.617284 0.875
23 AWU 0.6125 0.926471
24 CJB 0.603175 0.80597
25 UDX 0.597561 0.926471
26 UDP GAL 0.597561 0.898551
27 UAD 0.597561 0.926471
28 3UC 0.588235 0.875
29 USQ 0.583333 0.807692
30 UGB 0.583333 0.940298
31 UGA 0.583333 0.940298
32 5FU 0.57971 0.927536
33 G3N 0.576471 0.9
34 UGF 0.576471 0.887324
35 U3P 0.573529 0.953846
36 UA3 0.573529 0.953846
37 C 0.571429 0.941176
38 CAR 0.571429 0.941176
39 C5P 0.571429 0.941176
40 UDM 0.568182 0.9
41 5BU 0.56338 0.927536
42 U4S 0.557143 0.763889
43 UD2 0.555556 0.913043
44 UD1 0.555556 0.913043
45 CSQ 0.550562 0.863014
46 CSV 0.550562 0.863014
47 U2S 0.541667 0.777778
48 U3S 0.541667 0.763889
49 CNU 0.540541 0.941176
50 S5P 0.535211 0.901408
51 16B 0.534247 0.901408
52 FZK 0.530864 0.765432
53 U2P 0.528571 0.939394
54 UMP 0.527778 0.911765
55 DU 0.527778 0.911765
56 HP7 0.526882 0.926471
57 UD7 0.526882 0.913043
58 MJZ 0.521277 0.9
59 UP6 0.521127 0.884058
60 F5P 0.515789 0.9
61 12V 0.515789 0.887324
62 UD4 0.515789 0.9
63 F5G 0.515789 0.913043
64 HWU 0.515789 0.887324
65 BMP 0.513889 0.955224
66 UP5 0.510204 0.84
67 DKX 0.507246 0.732394
68 U6M 0.506849 0.969697
69 NUP 0.506849 0.927536
70 LSU 0.505882 0.746988
71 IUG 0.505155 0.797468
72 EPZ 0.5 0.9
73 JW5 0.5 0.955224
74 4TC 0.5 0.818182
75 U1S 0.5 0.76
76 EPU 0.49505 0.887324
77 EEB 0.49505 0.887324
78 UDZ 0.494949 0.84
79 H2U 0.486111 0.911765
80 YSU 0.483516 0.756098
81 6CN 0.480519 0.941176
82 OMP 0.480519 0.969697
83 6AU 0.480519 0.969697
84 TKW 0.48 0.927536
85 UMF 0.479452 0.869565
86 UUA 0.477612 0.757576
87 BMQ 0.472222 0.939394
88 PUP 0.47191 0.926471
89 5HM 0.467532 0.888889
90 O7E 0.463415 0.941176
91 ICR 0.460526 0.830986
92 UMA 0.458716 0.9
93 O7M 0.45679 0.941176
94 UC5 0.455696 0.885714
95 UTP U U U 0.454545 0.909091
96 CDP 0.45 0.927536
97 2TU 0.449275 0.760563
98 FNU 0.441558 0.876712
99 2TM 0.440476 0.888889
100 2QR 0.439655 0.810127
101 DUD 0.4375 0.898551
102 N3E 0.4375 0.743243
103 2OM 0.435897 0.925373
104 U21 0.434783 0.797468
105 U22 0.434783 0.777778
106 U20 0.434783 0.797468
107 HF4 0.433735 0.927536
108 CTP 0.433735 0.927536
109 DUT 0.433735 0.898551
110 8OP 0.428571 0.849315
111 BUP 0.428571 0.914286
112 8GM 0.421687 0.853333
113 5GW 0.420455 0.927536
114 CDP MG 0.414634 0.898551
115 4RA 0.414634 0.842105
116 0RC 0.413793 0.851351
117 DUP 0.411765 0.873239
118 DUN 0.409639 0.873239
119 UD0 0.408 0.831169
120 UM3 0.407895 0.897059
121 UVC 0.407895 0.842857
122 C5G 0.404255 0.875
123 6MZ C U 0.403226 0.775
124 UPA 0.401869 0.828947
125 UAG 0.4 0.851351
Similar Ligands (3D)
Ligand no: 1; Ligand: NAI; Similar ligands found: 4
No: Ligand Similarity coefficient
1 NAJ 0.9967
2 8ID 0.9651
3 NHD 0.9450
4 A7R 0.8646
Ligand no: 2; Ligand: U5P; Similar ligands found: 159
No: Ligand Similarity coefficient
1 CH 0.9980
2 PSU 0.9973
3 FN5 0.9948
4 TMP 0.9732
5 DUS 0.9718
6 DC 0.9664
7 DCM 0.9664
8 DDN 0.9644
9 DOC 0.9638
10 AMP 0.9607
11 PFU 0.9599
12 FDM 0.9594
13 UMC 0.9592
14 5IU 0.9586
15 NYM 0.9569
16 UFP 0.9556
17 QBT 0.9539
18 NIA 0.9524
19 C2R 0.9524
20 5CM 0.9522
21 BRU 0.9504
22 AMZ 0.9489
23 IRP 0.9478
24 IMP 0.9477
25 9L3 0.9467
26 AIR 0.9428
27 D4M 0.9413
28 2DT 0.9412
29 8BR 0.9372
30 LMS 0.9367
31 MZP 0.9362
32 RVP 0.9343
33 DA 0.9307
34 D5M 0.9307
35 FMP 0.9292
36 AS 0.9273
37 5GP 0.9224
38 5HU 0.9218
39 G 0.9216
40 NMN 0.9211
41 6MA 0.9211
42 NCN 0.9190
43 EO7 0.9189
44 IRN 0.9185
45 6RE 0.9182
46 J7C 0.9180
47 GAR 0.9171
48 XMP 0.9160
49 T3S 0.9160
50 DGP 0.9142
51 DG 0.9142
52 NEC 0.9123
53 M2T 0.9120
54 71V 0.9112
55 A3N 0.9101
56 IMU 0.9083
57 N5O 0.9067
58 Z8B 0.9047
59 6HW 0.9038
60 AOC 0.9029
61 ATM 0.9024
62 FAI 0.9014
63 EP4 0.9011
64 CTN 0.9002
65 JLN 0.8996
66 TDH 0.8991
67 6SY 0.8987
68 4UB 0.8973
69 7D5 0.8963
70 CMP 0.8944
71 BHF 0.8944
72 MTA 0.8934
73 PZB 0.8931
74 0SX 0.8928
75 TXS 0.8916
76 4ZK 0.8910
77 43J 0.8887
78 2T4 0.8886
79 XEZ 0.8883
80 9XZ 0.8879
81 362 0.8876
82 5QT 0.8869
83 FBP 0.8856
84 N8M 0.8853
85 O8M 0.8852
86 2GE 0.8842
87 NWQ 0.8838
88 CC7 0.8836
89 5UD 0.8830
90 VIB 0.8823
91 5AE 0.8814
92 I5A 0.8808
93 49K 0.8807
94 1TM 0.8807
95 IWH 0.8801
96 GEO 0.8799
97 103 0.8799
98 8OG 0.8796
99 43G 0.8783
100 SP1 0.8779
101 DRM 0.8774
102 URD 0.8759
103 14I 0.8755
104 RP1 0.8747
105 AFP 0.8738
106 6HV 0.8726
107 KWQ 0.8724
108 VKE 0.8724
109 HDU 0.8720
110 DUR 0.8710
111 K8W 0.8707
112 AHG 0.8702
113 90J 0.8699
114 1CE 0.8694
115 F01 0.8687
116 TYU 0.8678
117 FT1 0.8676
118 74Z 0.8675
119 6HZ 0.8674
120 HKK 0.8672
121 ML2 0.8669
122 F0G 0.8645
123 101 0.8644
124 PCG 0.8636
125 GG5 0.8631
126 3DV 0.8626
127 TYD 0.8621
128 T1D 0.8620
129 BL6 0.8617
130 HM5 0.8614
131 CA0 0.8614
132 CQU 0.8613
133 ADN 0.8606
134 YM6 0.8605
135 DCZ 0.8604
136 RVA 0.8603
137 T7O 0.8598
138 8G6 0.8596
139 HNA 0.8592
140 9W8 0.8591
141 YTZ 0.8588
142 4BH 0.8585
143 7MF 0.8580
144 K6B 0.8580
145 SW4 0.8576
146 ISJ 0.8576
147 ML1 0.8574
148 TBD 0.8568
149 ROL 0.8566
150 QTK 0.8555
151 K6N 0.8551
152 8RK 0.8549
153 YEX 0.8541
154 43F 0.8538
155 08D 0.8536
156 QTV 0.8529
157 JHY 0.8511
158 AD3 0.8509
159 90G 0.8508
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3PLN; Ligand: U5P; 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: 3pln.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3PLN; Ligand: U5P; 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: 3pln.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
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