Receptor
PDB id Resolution Class Description Source Keywords
4FJU 1.77 Å EC: 1.1.1.154 CRYSTAL STRUCTURE OF UREIDOGLYCOLATE DEHYDROGENASE IN TERNAR WITH NADH AND GLYOXYLATE ESCHERICHIA COLI ALLD NAD(P)H-DEPENDENT OXIDOREDUCTASE UREIDE PATHWAY UREIDOGLYCOLATE OXALURATE ANTIPARALLEL BETA-SHEET FOLD UREIDOGLYCOLATE DEHYDROGENASE OXIDOREDUCTASE
Ref.: STRUCTURAL AND FUNCTIONAL INSIGHTS INTO (S)-UREIDOG DEHYDROGENASE, A METABOLIC BRANCH POINT ENZYME IN N UTILIZATION. PLOS ONE V. 7 52066 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAI B:401;
A:401;
Valid;
Valid;
none;
none;
submit data
665.441 C21 H29 N7 O14 P2 c1nc(...
GLV A:402;
Valid;
none;
submit data
74.035 C2 H2 O3 C(=O)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4FJU 1.77 Å EC: 1.1.1.154 CRYSTAL STRUCTURE OF UREIDOGLYCOLATE DEHYDROGENASE IN TERNAR WITH NADH AND GLYOXYLATE ESCHERICHIA COLI ALLD NAD(P)H-DEPENDENT OXIDOREDUCTASE UREIDE PATHWAY UREIDOGLYCOLATE OXALURATE ANTIPARALLEL BETA-SHEET FOLD UREIDOGLYCOLATE DEHYDROGENASE OXIDOREDUCTASE
Ref.: STRUCTURAL AND FUNCTIONAL INSIGHTS INTO (S)-UREIDOG DEHYDROGENASE, A METABOLIC BRANCH POINT ENZYME IN N UTILIZATION. PLOS ONE V. 7 52066 2012
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4FJU - GLV C2 H2 O3 C(=O)C(=O)....
2 4H8A - NAI C21 H29 N7 O14 P2 c1nc(c2c(n....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4FJU - GLV C2 H2 O3 C(=O)C(=O)....
2 4H8A - NAI C21 H29 N7 O14 P2 c1nc(c2c(n....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1VBI - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
2 1V9N - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
3 4FJU - GLV C2 H2 O3 C(=O)C(=O)....
4 4H8A - NAI C21 H29 N7 O14 P2 c1nc(c2c(n....
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: GLV; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 GLV 1 1
2 MAE 0.5 0.666667
3 FUM 0.5 0.666667
4 OXD 0.416667 0.75
5 CCU 0.411765 0.666667
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: GLV; Similar ligands found: 247
No: Ligand Similarity coefficient
1 PPI 1.0261
2 GLY 1.0257
3 NHY 1.0000
4 HAE 1.0000
5 MGX 1.0000
6 HVB 1.0000
7 AGU 1.0000
8 R3W 1.0000
9 NMU 1.0000
10 TSZ 1.0000
11 61G 1.0000
12 AKR 1.0000
13 F50 1.0000
14 NIE 1.0000
15 J3K 1.0000
16 ALA 1.0000
17 2A1 1.0000
18 2A3 1.0000
19 F3V 1.0000
20 FAH 1.0000
21 GOA 1.0000
22 ATO 0.9965
23 BXA 0.9915
24 1BP 0.9885
25 BRP 0.9870
26 CP2 0.9773
27 PXO 0.9773
28 GOL 0.9768
29 NIS 0.9760
30 TCV 0.9734
31 LAC 0.9704
32 AOA 0.9695
33 OXL 0.9690
34 OXM 0.9688
35 PYR 0.9687
36 BUA 0.9677
37 2OP 0.9676
38 PYM 0.9675
39 3OH 0.9672
40 HGY 0.9671
41 GXV 0.9670
42 3TR 0.9670
43 BU4 0.9662
44 2AI 0.9662
45 DAL 0.9655
46 HOW 0.9641
47 GBL 0.9638
48 NAK 0.9637
49 1MZ 0.9636
50 4MZ 0.9636
51 ALQ 0.9631
52 6SP 0.9630
53 HBS 0.9630
54 2MZ 0.9626
55 BUO 0.9625
56 5MP 0.9624
57 MR3 0.9619
58 HBR 0.9614
59 3GR 0.9609
60 BAQ 0.9602
61 3MT 0.9597
62 1CB 0.9585
63 MZY 0.9584
64 9A4 0.9580
65 SAR 0.9570
66 5KX 0.9568
67 TRI 0.9567
68 AF3 0.9565
69 ACT 0.9564
70 BAL 0.9563
71 ACM 0.9554
72 JZ6 0.9552
73 SEY 0.9537
74 5Y9 0.9532
75 ETF 0.9527
76 MEU 0.9526
77 ABA 0.9526
78 IMD 0.9523
79 BUQ 0.9523
80 AMT 0.9521
81 BMD 0.9519
82 2HA 0.9517
83 EGD 0.9511
84 AXO 0.9509
85 EDO 0.9506
86 PZO 0.9501
87 MMU 0.9501
88 HUH 0.9493
89 3ZS 0.9486
90 3CL 0.9476
91 OSM 0.9465
92 BYZ 0.9457
93 ATQ 0.9456
94 NOE 0.9434
95 ES3 0.9426
96 TAN 0.9413
97 CRD 0.9411
98 XAP 0.9399
99 CNH 0.9398
100 78T 0.9383
101 ALF 0.9374
102 CYS 0.9367
103 IPA 0.9363
104 MTG 0.9354
105 BEF 0.9352
106 BUB 0.9351
107 SLP 0.9345
108 BRJ 0.9341
109 2PO 0.9341
110 PYZ 0.9330
111 P1R 0.9321
112 HSW 0.9320
113 TB0 0.9319
114 VSO 0.9318
115 9A7 0.9316
116 TF4 0.9301
117 HYN 0.9298
118 3BB 0.9292
119 BNZ 0.9289
120 XIX 0.9281
121 0PY 0.9280
122 13D 0.9269
123 QPT 0.9262
124 B20 0.9261
125 KCS 0.9256
126 D2P 0.9233
127 0CL 0.9230
128 PHZ 0.9225
129 MZ0 0.9225
130 KG7 0.9216
131 ITU 0.9178
132 DE2 0.9170
133 DXX 0.9168
134 1AC 0.9162
135 SER 0.9152
136 2RA 0.9147
137 DSN 0.9139
138 3BR 0.9136
139 MB3 0.9126
140 A3B 0.9126
141 DBB 0.9126
142 FW5 0.9123
143 2KT 0.9121
144 3PY 0.9119
145 7EX 0.9117
146 25T 0.9114
147 NVI 0.9113
148 BXO 0.9101
149 24T 0.9101
150 THR 0.9099
151 DGY 0.9094
152 03W 0.9094
153 DMI 0.9086
154 HUI 0.9083
155 CHT 0.9082
156 HIU 0.9076
157 MSF 0.9065
158 CEJ 0.9061
159 MMZ 0.9061
160 MCH 0.9049
161 9PO 0.9047
162 CXL 0.9046
163 CYH 0.9046
164 MMQ 0.9043
165 DCE 0.9042
166 A2Q 0.9036
167 HVK 0.9035
168 HSL 0.9030
169 HRZ 0.9030
170 LGA 0.9030
171 2AP 0.9028
172 1SP 0.9026
173 HAI 0.9023
174 V1L 0.9018
175 DTI 0.9018
176 PRI 0.9016
177 BVG 0.9005
178 BVC 0.9001
179 8FH 0.8997
180 L60 0.8995
181 IPH 0.8991
182 FJO 0.8988
183 3AP 0.8984
184 MBN 0.8984
185 39J 0.8984
186 4AP 0.8982
187 VN4 0.8980
188 4AX 0.8980
189 1DH 0.8980
190 2IM 0.8978
191 MLI 0.8978
192 MLA 0.8978
193 E60 0.8977
194 SMB 0.8975
195 DMG 0.8973
196 HV2 0.8971
197 ETX 0.8957
198 MLM 0.8957
199 C2N 0.8955
200 PIH 0.8954
201 PUT 0.8950
202 DCY 0.8945
203 C5J 0.8943
204 2EZ 0.8941
205 WOT 0.8941
206 93B 0.8940
207 TMO 0.8939
208 KSW 0.8938
209 03S 0.8935
210 ETM 0.8934
211 MTD 0.8934
212 BTL 0.8923
213 GXE 0.8910
214 TAY 0.8909
215 XPO 0.8904
216 PPF 0.8898
217 HVQ 0.8891
218 8CL 0.8885
219 AAE 0.8860
220 TAU 0.8857
221 HHN 0.8850
222 3HR 0.8848
223 FPO 0.8826
224 2HP 0.8826
225 HLT 0.8818
226 3HL 0.8817
227 GB 0.8808
228 8X3 0.8806
229 TTO 0.8806
230 TBU 0.8803
231 IVA 0.8799
232 FUS 0.8787
233 HGW 0.8781
234 COM 0.8758
235 PO4 0.8757
236 2HE 0.8755
237 BF4 0.8745
238 DSS 0.8739
239 POA 0.8732
240 2PA 0.8731
241 9SB 0.8702
242 ISU 0.8701
243 WO6 0.8695
244 P2D 0.8666
245 9XN 0.8660
246 280 0.8597
247 EFS 0.8545
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4FJU; Ligand: NAI; Similar sites found with APoc: 7
This union binding pocket(no: 1) in the query (biounit: 4fju.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
1 1Z2I NAD 41.0256
2 1Z2I NAD 41.0256
3 2X06 NAD 48.5465
4 2X06 NAD 48.5465
5 2X06 NAD 48.5465
6 2X06 NAD 48.5465
7 2X06 NAD 48.5465
Pocket No.: 2; Query (leader) PDB : 4FJU; Ligand: GLV; Similar sites found with APoc: 6
This union binding pocket(no: 2) in the query (biounit: 4fju.bio1) has 32 residues
No: Leader PDB Ligand Sequence Similarity
1 1Z2I NAD 41.0256
2 1Z2I NAD 41.0256
3 2X06 NAD 48.5465
4 2X06 NAD 48.5465
5 2X06 NAD 48.5465
6 2X06 NAD 48.5465
Pocket No.: 3; Query (leader) PDB : 4FJU; Ligand: NAI; Similar sites found with APoc: 8
This union binding pocket(no: 3) in the query (biounit: 4fju.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
1 1Z2I NAD 41.0256
2 1Z2I NAD 41.0256
3 2X06 NAD 48.5465
4 2X06 NAD 48.5465
5 2X06 NAD 48.5465
6 2X06 NAD 48.5465
7 2X06 NAD 48.5465
8 2X06 NAD 48.5465
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