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 3 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
Ligand no: 1; Ligand: NAI; Similar ligands found: 249
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 6V0 0.649123 0.986842
9 TXE 0.62931 0.948052
10 BA3 0.628866 0.933333
11 AP5 0.622449 0.933333
12 B4P 0.622449 0.933333
13 TXD 0.62069 0.923077
14 APR 0.613861 0.907895
15 AR6 0.613861 0.907895
16 EAD 0.609375 0.961538
17 AGS 0.607843 0.8625
18 SAP 0.607843 0.8625
19 ADP 0.606061 0.907895
20 ATP 0.60396 0.907895
21 50T 0.60396 0.871795
22 AN2 0.6 0.896104
23 A22 0.598131 0.921053
24 5FA 0.598039 0.907895
25 AQP 0.598039 0.907895
26 CA0 0.594059 0.909091
27 M33 0.594059 0.896104
28 AD9 0.592233 0.884615
29 NAJ PZO 0.592 0.935897
30 P1H 0.590909 0.9375
31 ACP 0.588235 0.884615
32 A1R 0.587156 0.851852
33 4AD 0.587156 0.886076
34 PRX 0.582524 0.8375
35 ANP 0.580952 0.884615
36 3OD 0.580357 0.909091
37 SRP 0.579439 0.873418
38 ADX 0.578431 0.821429
39 OAD 0.576577 0.909091
40 5AL 0.575472 0.896104
41 ADJ 0.569106 0.890244
42 UP5 0.566667 0.960526
43 ACQ 0.566038 0.884615
44 AMP 0.561224 0.881579
45 A 0.561224 0.881579
46 ATF 0.555556 0.873418
47 8QN 0.54955 0.896104
48 25L 0.547826 0.921053
49 4TC 0.544715 0.935897
50 ADQ 0.544643 0.909091
51 PAJ 0.544643 0.853659
52 AMO 0.544643 0.897436
53 ABM 0.544554 0.858974
54 NPW 0.544 0.949367
55 WAQ 0.54386 0.851852
56 PR8 0.54386 0.821429
57 LAD 0.54386 0.831325
58 DG1 0.541353 0.986842
59 1DG 0.541353 0.986842
60 00A 0.539823 0.875
61 NZQ 0.539683 0.974026
62 1ZZ 0.53913 0.811765
63 BIS 0.53913 0.851852
64 APC 0.537736 0.873418
65 OMR 0.536585 0.823529
66 5SV 0.535714 0.797619
67 OOB 0.535714 0.921053
68 25A 0.535714 0.907895
69 3UK 0.535088 0.909091
70 AMP MG 0.534653 0.835443
71 AP2 0.533981 0.873418
72 A12 0.533981 0.873418
73 NXX 0.528455 0.922078
74 DND 0.528455 0.922078
75 CNA 0.527559 0.922078
76 AHX 0.526316 0.864198
77 DLL 0.526316 0.921053
78 FYA 0.525862 0.871795
79 NB8 0.525862 0.864198
80 ME8 0.525862 0.811765
81 PTJ 0.525862 0.841463
82 YAP 0.525424 0.886076
83 SRA 0.524752 0.8375
84 SON 0.52381 0.873418
85 TAT 0.522936 0.873418
86 VO4 ADP 0.522523 0.871795
87 ADP VO4 0.522523 0.871795
88 48N 0.520325 0.864198
89 YLP 0.520325 0.793103
90 YLB 0.52 0.793103
91 AU1 0.518868 0.884615
92 ADP MG 0.518868 0.848101
93 ADP PO3 0.518519 0.881579
94 9SN 0.516949 0.864198
95 BEF ADP 0.514019 0.82716
96 ADP BEF 0.514019 0.82716
97 ATP MG 0.513761 0.848101
98 TXA 0.512821 0.897436
99 FA5 0.512605 0.897436
100 GAP 0.509091 0.860759
101 4UU 0.508197 0.960526
102 YLC 0.507937 0.833333
103 T5A 0.507812 0.925926
104 RBY 0.504587 0.873418
105 ADV 0.504587 0.873418
106 4UW 0.504 0.924051
107 TXP 0.503876 0.911392
108 DAL AMP 0.5 0.871795
109 ALF ADP 0.5 0.817073
110 G3A 0.5 0.8875
111 TYM 0.5 0.897436
112 ADP ALF 0.5 0.817073
113 LAQ 0.5 0.811765
114 COD 0.496183 0.786517
115 YLA 0.496124 0.813953
116 139 0.496124 0.9125
117 AFH 0.495935 0.853659
118 G5P 0.495935 0.8875
119 XAH 0.495868 0.811765
120 ANP MG 0.495575 0.839506
121 BT5 0.492424 0.784091
122 AYB 0.492308 0.784091
123 A4P 0.492188 0.880952
124 GTA 0.491935 0.855422
125 4UV 0.491803 0.960526
126 A2R 0.491228 0.896104
127 MAP 0.486957 0.8625
128 XNP 0.484848 0.936709
129 NAD 0.484848 0.921053
130 UPA 0.484375 0.948052
131 7MD 0.483871 0.833333
132 MYR AMP 0.483333 0.790698
133 NA7 0.483051 0.873418
134 YLY 0.477941 0.784091
135 ATR 0.477477 0.881579
136 LA8 ALF 3PG 0.476562 0.809524
137 ALF ADP 3PG 0.476562 0.809524
138 AOC 0.47619 0.792208
139 ATP A A A 0.47541 0.894737
140 BTX 0.473684 0.793103
141 5AS 0.472222 0.736264
142 TYR AMP 0.471545 0.873418
143 NAQ 0.471014 0.864198
144 ADP BMA 0.470588 0.884615
145 N0B 0.467626 0.835294
146 A A 0.466667 0.883117
147 A3D 0.466667 0.909091
148 NJP 0.466165 0.910256
149 IOT 0.465649 0.784091
150 AF3 ADP 3PG 0.465116 0.809524
151 PAP 0.464286 0.894737
152 NAE 0.463768 0.886076
153 7MC 0.461538 0.813953
154 DZD 0.459259 0.876543
155 ZID 0.457143 0.909091
156 TAD 0.456693 0.853659
157 2A5 0.455357 0.8375
158 62F 0.453947 0.833333
159 AHZ 0.453125 0.790698
160 FB0 0.452055 0.76087
161 JB6 0.45082 0.851852
162 ITT 0.45045 0.857143
163 7D4 0.45045 0.825
164 LPA AMP 0.449612 0.790698
165 G5A 0.447368 0.755556
166 M24 0.446043 0.843373
167 AVV 0.445378 0.841463
168 NAD IBO 0.444444 0.8625
169 NDC 0.442177 0.864198
170 ARG AMP 0.44186 0.781609
171 NSS 0.441667 0.775281
172 4TA 0.441176 0.890244
173 VMS 0.440678 0.764045
174 54H 0.440678 0.764045
175 7D3 0.440367 0.825
176 5CD 0.44 0.753247
177 PPS 0.439655 0.8
178 RAB 0.438776 0.789474
179 ADN 0.438776 0.789474
180 XYA 0.438776 0.789474
181 NDE 0.438356 0.897436
182 AR6 AR6 0.4375 0.883117
183 TSB 0.436975 0.793103
184 53H 0.436975 0.755556
185 DTA 0.436893 0.759494
186 A3P 0.436364 0.881579
187 A2P 0.436364 0.868421
188 A5A 0.435897 0.781609
189 FNK 0.435065 0.840909
190 ODP 0.433824 0.924051
191 SFG 0.433628 0.725
192 Z5A 0.433566 0.858824
193 6FA 0.433333 0.835294
194 SSA 0.432203 0.775281
195 J7C 0.431193 0.702381
196 DTP 0.431034 0.825
197 P5A 0.430894 0.723404
198 5N5 0.43 0.766234
199 DSZ 0.429752 0.775281
200 LSS 0.429752 0.73913
201 NAJ PYZ 0.429577 0.843373
202 52H 0.428571 0.755556
203 SFD 0.427632 0.731959
204 6AD 0.42735 0.831325
205 EP4 0.427184 0.707317
206 FDA 0.426667 0.870588
207 ARU 0.42623 0.788235
208 NVA LMS 0.42623 0.73913
209 6RE 0.425926 0.694118
210 A4D 0.425743 0.766234
211 5CA 0.425 0.775281
212 3DH 0.424528 0.725
213 AV2 0.423729 0.835443
214 LEU LMS 0.422764 0.73913
215 AMP DBH 0.421875 0.860759
216 DAT 0.421053 0.825
217 5X8 0.421053 0.7375
218 GSU 0.419355 0.755556
219 MTA 0.419048 0.725
220 3AT 0.418803 0.883117
221 DCA 0.41844 0.777778
222 ETB 0.41844 0.786517
223 FAS 0.418301 0.845238
224 FAD 0.418301 0.845238
225 A3N 0.418182 0.759494
226 F2N 0.417178 0.850575
227 7D5 0.415094 0.8
228 A U 0.414815 0.910256
229 YSA 0.414062 0.775281
230 NAD BBN 0.412903 0.835294
231 0T1 0.412587 0.777778
232 2AM 0.411215 0.857143
233 M2T 0.409524 0.690476
234 KAA 0.408 0.731183
235 7C5 0.407692 0.790123
236 3AM 0.407407 0.844156
237 AMP NAD 0.406897 0.873418
238 NAP 0.406897 0.909091
239 PUA 0.405594 0.9
240 FAY 0.405063 0.855422
241 P5F 0.404908 0.83908
242 EEM 0.403361 0.670455
243 COA 0.402778 0.777778
244 RFL 0.402516 0.816092
245 GJV 0.401786 0.686047
246 SA8 0.401709 0.686047
247 U A C C 0.401408 0.898734
248 G A A A 0.4 0.841463
249 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 FUM 0.5 0.666667
3 MAE 0.5 0.666667
4 OXD 0.416667 0.75
5 CCU 0.411765 0.666667
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4FJU; Ligand: NAI; 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: 4fju.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4FJU; Ligand: GLV; Similar sites found: 23
This union binding pocket(no: 2) in the query (biounit: 4fju.bio1) has 32 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3UEC ALA ARG TPO LYS 0.01342 0.43534 None
2 4C2C ALA ALA ALA 0.02789 0.41633 3.1339
3 5LFV SIA GAL NAG 0.01495 0.43648 3.15457
4 2G30 ALA ALA PHE 0.006171 0.46951 3.87597
5 3B6R CRN 0.01144 0.4201 4.8433
6 2BVE PH5 0.04904 0.40271 5.04202
7 2UVO NAG 0.02686 0.40689 5.26316
8 2UVO NDG 0.0292 0.40445 5.26316
9 4YG0 GAL NAG GAL BGC 0.03011 0.41092 5.4878
10 1KC7 PPR 0.02389 0.4132 5.69801
11 3PDT ADP 0.02201 0.40373 5.81818
12 3ALN ANP 0.01763 0.40503 6.11621
13 1WQ1 AF3 0.02758 0.41727 8.43373
14 3H0L ADP 0.04156 0.40031 9.68661
15 5L3S G 0.04995 0.40429 9.73154
16 5LOL GSH 0.02149 0.42043 10.6977
17 1FQJ ALF 0.04668 0.40177 12.2449
18 1FQK ALF 0.04765 0.40161 12.2449
19 1S20 NAD 0.0000001582 0.62774 31.9088
20 1Z2I NAD 0.00000000007769 0.70529 41.0256
21 2CWH PYC 0.000000007745 0.61337 44.3149
22 2CWH NDP 0.00000002004 0.58225 44.3149
23 2X06 NAD 0.00000000006486 0.74191 48.5465
Pocket No.: 3; Query (leader) PDB : 4FJU; Ligand: NAI; Similar sites found: 39
This union binding pocket(no: 3) in the query (biounit: 4fju.bio1) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3UEC ALA ARG TPO LYS 0.01279 0.43534 None
2 2DVZ GLU 0.01876 0.41326 1.91083
3 1QXA GLY GLY GLY 0.005742 0.46633 2.12766
4 3CV2 OXL 0.03549 0.40579 2.5641
5 5CFT APC 0.009066 0.40749 2.7027
6 4NZ6 DGL 0.006444 0.44888 2.8754
7 4C2C ALA ALA ALA 0.02668 0.41633 3.1339
8 5LFV SIA GAL NAG 0.01427 0.43648 3.15457
9 5E5U MLI 0.006665 0.44387 3.40909
10 5XG5 A2G 0.03713 0.409 3.44828
11 5FJJ MAN 0.01539 0.45455 3.7037
12 2G30 ALA ALA PHE 0.005904 0.46951 3.87597
13 2OX9 GAL NAG FUC 0.03232 0.4113 4.28571
14 2BVE PH5 0.04702 0.40271 5.04202
15 2UVO NAG 0.02569 0.40689 5.26316
16 4YG0 GAL NAG GAL BGC 0.02307 0.41516 5.4878
17 1KC7 PPR 0.02891 0.41715 5.69801
18 3JUC PCA 0.04408 0.40406 5.88235
19 2CXG GLC GLC 0.01419 0.4302 6.83761
20 5F90 LMR 0.02083 0.42776 7.05128
21 5F90 GLA GAL 0.02224 0.42473 7.05128
22 5F90 GLA GAL BGC 5VQ 0.02664 0.41933 7.05128
23 2X1L ADN 0.01546 0.41001 7.69231
24 4L80 OXL 0.004016 0.46785 8.04598
25 3NOJ PYR 0.004634 0.46355 8.40336
26 3H0L ADP 0.03956 0.40031 9.68661
27 5L3S G 0.008218 0.44547 9.73154
28 1D8C GLV 0.004579 0.43687 9.97151
29 2J5V PCA 0.01354 0.42558 9.97151
30 2EB5 OXL 0.02404 0.41497 10.1124
31 1FQK ALF 0.04194 0.40372 12.2449
32 1FQJ ALF 0.04743 0.40079 12.2449
33 5FUI APY 0.01146 0.43424 21.2121
34 1S20 NAD 0.00000003128 0.65742 31.9088
35 2VOH CIT 0.01834 0.41091 38.4615
36 1Z2I NAD 0.00000000001881 0.72653 41.0256
37 2CWH NDP 0.000000007195 0.60789 44.3149
38 2CWH PYC 0.00000001622 0.60702 44.3149
39 2X06 NAD 0.00000000001586 0.76473 48.5465
Feedback