Receptor
PDB id Resolution Class Description Source Keywords
4LCQ 1.81 Å EC: 7.-.-.- THE CRYSTAL STRUCTURE OF DI-ZN DIHYDROPYRIMIDINASE IN COMPLE NCBI TETRAODON NIGROVIRIDIS HYDROLASE ZINC BINDING CARBOXYLATION ALPHA-BETA BARREL HACTIVATOR
Ref.: CRYSTAL STRUCTURES OF VERTEBRATE DIHYDROPYRIMIDINAS COMPLEXES FROM TETRAODON NIGROVIRIDIS WITH LYSINE CARBAMYLATION: METAL AND STRUCTURAL REQUIREMENTS FO POST-TRANSLATIONAL MODIFICATION AND FUNCTION. J.BIOL.CHEM. V. 288 30645 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN A:602;
A:601;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
URQ A:603;
Valid;
none;
submit data
146.144 C5 H10 N2 O3 C[C@@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4LCQ 1.81 Å EC: 7.-.-.- THE CRYSTAL STRUCTURE OF DI-ZN DIHYDROPYRIMIDINASE IN COMPLE NCBI TETRAODON NIGROVIRIDIS HYDROLASE ZINC BINDING CARBOXYLATION ALPHA-BETA BARREL HACTIVATOR
Ref.: CRYSTAL STRUCTURES OF VERTEBRATE DIHYDROPYRIMIDINAS COMPLEXES FROM TETRAODON NIGROVIRIDIS WITH LYSINE CARBAMYLATION: METAL AND STRUCTURAL REQUIREMENTS FO POST-TRANSLATIONAL MODIFICATION AND FUNCTION. J.BIOL.CHEM. V. 288 30645 2013
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 250 families.
1 4LCQ - URQ C5 H10 N2 O3 C[C@@H](CN....
2 4LCR - URP C4 H8 N2 O3 C(CNC(=O)N....
3 4LCS - HYN C3 H4 N2 O2 C1C(=O)NC(....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 217 families.
1 4LCQ - URQ C5 H10 N2 O3 C[C@@H](CN....
2 4LCR - URP C4 H8 N2 O3 C(CNC(=O)N....
3 4LCS - HYN C3 H4 N2 O2 C1C(=O)NC(....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 181 families.
1 4LCQ - URQ C5 H10 N2 O3 C[C@@H](CN....
2 4LCR - URP C4 H8 N2 O3 C(CNC(=O)N....
3 4LCS - HYN C3 H4 N2 O2 C1C(=O)NC(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: URQ; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 URQ 1 1
2 CDV 0.40625 0.638889
3 UGC 0.4 0.648649
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4LCQ; Ligand: URQ; Similar sites found: 311
This union binding pocket(no: 1) in the query (biounit: 4lcq.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1BTN I3P 0.0166 0.45111 None
2 1UO5 PIH 0.02259 0.4418 None
3 3KPE TM3 0.01378 0.41911 None
4 1N6B DMZ 0.000004323 0.42414 1.05708
5 1Q11 TYE 0.0004014 0.47586 1.07527
6 4W6Z 8ID 0.04927 0.40053 1.15274
7 2QF7 COA 0.007376 0.40329 1.15385
8 3FS8 ACO 0.004529 0.40957 1.4652
9 1Y42 TYR 0.009992 0.41519 1.53061
10 1PEA ACM 0.03818 0.40858 1.55844
11 1A5Z OXM 0.0008894 0.49047 1.5674
12 1A5Z FBP 0.0004159 0.43252 1.5674
13 3NKT 1HN 0.00003782 0.44099 1.63043
14 2BLE 5GP 0.00005022 0.46413 1.63488
15 2WL9 MBD 0.000002584 0.48609 1.63934
16 4WBD ADP 0.009668 0.43219 1.73077
17 2P2V CSF 0.0000007 0.40279 1.73611
18 4P87 4NP 0.00001566 0.45247 1.74564
19 1BGV GLU 0.00001772 0.40312 1.78174
20 3TFC PEP 0.01117 0.41308 1.81818
21 2NVK NAP 0.005205 0.42752 1.84426
22 2IMP NAI 0.00002646 0.48633 1.87891
23 4C25 13P 0.0005047 0.40084 1.88679
24 1SJD NPG 0.000976 0.40511 1.90217
25 1ZOA 140 0.04174 0.4044 1.90275
26 4IVG ANP 0.000005251 0.48733 1.92308
27 4CCO OGA 0.003414 0.43548 1.92719
28 2Z5Y HRM 0.0001502 0.41592 1.94932
29 2PP3 LGT 0.001273 0.43274 2.01005
30 2YYJ 4HP 0.003145 0.41719 2.079
31 2YYJ FAD 0.003145 0.41719 2.079
32 2OWZ F6P 0.0001038 0.43508 2.10843
33 2OWZ CIT 0.00008258 0.40414 2.10843
34 1H16 PYR 0.02081 0.42193 2.11538
35 4RJK PYR 0.02827 0.41521 2.11538
36 1G6O ADP 0.0002702 0.43697 2.12121
37 4PB2 5UD 0.0001496 0.4527 2.12264
38 1LDM NAD 0.000046 0.46888 2.12766
39 1QW9 KHP 0.00002163 0.43051 2.19124
40 4G1V FAD 0.0007281 0.445 2.25564
41 1TV5 ORO 0.0001316 0.46239 2.25734
42 1TV5 A26 0.0001844 0.43595 2.25734
43 1TV5 N8E 0.002993 0.40642 2.25734
44 1H0C AOA 0.003484 0.45356 2.29592
45 4AF0 IMP 0.00003152 0.46055 2.30769
46 2YIV YIV 0.007216 0.44503 2.30769
47 4AF0 MOA 0.00008692 0.40997 2.30769
48 2YIV NBN 0.04196 0.40121 2.30769
49 3CKZ ZMR 0.00009916 0.43816 2.33766
50 4OB6 S2T 0.001326 0.42747 2.34604
51 3UXL CFI 0.000002063 0.41918 2.34987
52 1RM4 NDP 0.000172 0.44678 2.37389
53 4ZNO SUC 0.04349 0.40515 2.38806
54 1QDS PGA 0.01097 0.40449 2.39044
55 2QS8 MET 0.00001761 0.43674 2.39234
56 4KCT FDP 0.002791 0.42407 2.40481
57 3O03 NAP 0.001286 0.41687 2.4055
58 4NAO AKG 0.006487 0.44055 2.45399
59 1K27 MTM 0.0000965 0.40921 2.4735
60 1F1V DHY 0.003766 0.4284 2.47678
61 1YRX FMN 0.008412 0.40108 2.47934
62 1VCO GLN 0.0000136 0.45431 2.5
63 1LTH NAD 0.0006243 0.42358 2.50784
64 1XMV ADP 0.0001191 0.4455 2.52809
65 1JN2 SFP 0.002423 0.42196 2.53165
66 3P3N AKG 0.005479 0.43776 2.5788
67 2WA4 069 0.005732 0.41165 2.5788
68 1VQ2 DDN 0.000008711 0.49074 2.59067
69 3DER ALA LYS 0.002866 0.40346 2.6087
70 3RO7 TDR 0.0000537 0.48439 2.64151
71 1WNG SAH 0.001384 0.41443 2.64151
72 1RZM PEP 0.009957 0.41525 2.66272
73 2ZI8 SDT 0.0001304 0.41769 2.66667
74 1YBH FAD 0.0003276 0.45306 2.69231
75 1YBH P22 0.0001072 0.42339 2.69231
76 2Q8H TF4 0.009477 0.44628 2.7027
77 2FR6 CTN 0.001675 0.41539 2.73973
78 3FPZ AHZ 0.00003651 0.4816 2.76074
79 2BO4 FLC 0.009038 0.4336 2.77078
80 1R0X ATP 0.000108 0.42635 2.7972
81 4KS1 2H8 0.0003641 0.42309 2.82051
82 4QCK ASD 0.000003455 0.47705 2.84974
83 2EG7 OTD 0.000002348 0.54642 2.88184
84 3WE0 FAD 0.001062 0.40874 2.88462
85 3F3E LEU 0.0006273 0.40904 2.89017
86 1SQ5 PAU 0.005578 0.42621 2.92208
87 2YP9 SIA CMO 0.002692 0.4139 2.98211
88 3OIG IMJ 0.000000904 0.48737 3.00752
89 3OIG NAD 0.00004925 0.46441 3.00752
90 4MOB ADP 0.0007378 0.4347 3.01205
91 4A3R CIT 0.000004125 0.47136 3.02326
92 2BJF DXC 0.000002867 0.41273 3.03951
93 3WIR BGC 0.006459 0.4177 3.07692
94 2JC9 ADN 0.01737 0.4047 3.07692
95 1O7N IND 0.00007304 0.40757 3.09278
96 1Y7P RIP 0.009194 0.4273 3.13901
97 2IZ1 ATR 0.001418 0.46503 3.16456
98 1H6W SER LEU ASN TYR ILE ILE LYS VAL LYS GLU 0.001388 0.41035 3.20513
99 3K9W ADE 0.002686 0.42527 3.20856
100 3K9W 4PS 0.002686 0.42527 3.20856
101 1FA2 DOM 0.000003289 0.46348 3.21285
102 1V5F FAD 0.002225 0.44334 3.26923
103 1V5F TPP 0.002225 0.44334 3.26923
104 1CKM GTP 0.001576 0.44433 3.33333
105 4QDC ASD 0.00003136 0.44137 3.33333
106 3NOJ PYR 0.0006165 0.47108 3.36134
107 1FNZ A2G 0.001436 0.40656 3.37553
108 3TA2 AKG 0.0002673 0.40875 3.38983
109 1Z34 2FD 0.0004252 0.42797 3.40426
110 1MZV AMP 0.009233 0.40756 3.40426
111 4LHM AZZ 0.02172 0.40497 3.40909
112 1OMZ UD2 0.0001988 0.4312 3.41297
113 2Y6P CTP 0.003274 0.42599 3.4188
114 4TSK NDP 0.003299 0.40366 3.42857
115 1EB9 HBA 0.005357 0.41282 3.43511
116 1ZFJ IMP 0.003729 0.42078 3.46232
117 2GN2 C5P 0.00009636 0.4647 3.50877
118 4M7F BM3 0.00002386 0.52906 3.53982
119 1O6B ADP 0.0006762 0.41583 3.5503
120 4LTN NAI 0.0003972 0.42604 3.5533
121 2ZJF BSU 0.002431 0.43127 3.59116
122 2XD9 XD9 0.00006783 0.49661 3.59281
123 1BDB NAD 0.0002688 0.44817 3.61011
124 1JA9 PYQ 0.00001844 0.44202 3.64964
125 1JA9 NDP 0.0004001 0.44099 3.64964
126 2W8Q SIN 0.000008159 0.42005 3.6961
127 1A78 TDG 0.01317 0.40604 3.73134
128 1ZJ6 G3D 0.0102 0.40169 3.74332
129 2HFK E4H 0.009743 0.41566 3.76176
130 1PX8 XYP 0.01082 0.41864 3.8
131 4HE2 AMP 0.000003139 0.4538 3.84615
132 1RP0 AHZ 0.000007287 0.49873 3.87324
133 3VCA PRO 0.0003196 0.48367 3.8835
134 2XDQ MGX 0.04448 0.411 3.91304
135 1FX8 BOG 0.00003579 0.4804 3.91459
136 1D09 PAL 0.004566 0.42129 3.92157
137 1I9G SAM 0.00001148 0.47192 3.92857
138 4JWX 1N4 0.01832 0.40369 3.92857
139 2DWU DGL 0.005162 0.42263 3.98551
140 2H6B 3C4 0.0003572 0.43309 4
141 1FS5 TLA 0.00007886 0.41939 4.13534
142 2J5S KTA 0.0001112 0.45728 4.18251
143 4JP3 CIT 0.004374 0.41632 4.1841
144 1XX4 BAM 0.0002812 0.48611 4.21456
145 3CL7 HYN 0.00001498 0.4306 4.22078
146 4NVP 7CH 0.00002428 0.44849 4.30622
147 2VDJ HSE 0.005405 0.45132 4.31894
148 3SHR CMP 0.001381 0.44131 4.34783
149 2NZ2 ASP 0.00005574 0.51307 4.35835
150 2NZ2 CIR 0.000378 0.411 4.35835
151 2C9O ADP 0.0001016 0.40889 4.38596
152 4OYA 1VE 0.00737 0.41134 4.46809
153 2EB5 OXL 0.01475 0.41772 4.49438
154 3PHQ KDO 0.005544 0.486 4.5045
155 2C5S AMP 0.008728 0.413 4.60048
156 3A1I UNU 0.005287 0.41748 4.61538
157 1T10 F6P 0.01198 0.41665 4.61538
158 5T63 ALA ALA ALA ALA 0.001968 0.40205 4.63215
159 4B9E FAH 0.003793 0.45178 4.65116
160 4CMF PXG 0.0000936 0.4478 4.65839
161 1YOE RIB 0.00001437 0.44513 4.65839
162 4B7J G39 0.0002769 0.41434 4.69083
163 4TMK T5A 0.0007705 0.45004 4.69484
164 3MB5 SAM 0.00000247 0.49768 4.70588
165 3K3G MMU 0.001609 0.4527 4.70588
166 1A8S PPI 0.009354 0.40523 4.7619
167 1XIU REA 0.0006195 0.4352 4.78261
168 4KCF AKM 0.00001039 0.47796 4.84582
169 4KCF FMN 0.0001253 0.43004 4.84582
170 3IU9 T07 0.0003267 0.43691 4.86111
171 1Y0L HAN 0.03196 0.42541 4.86726
172 2FWP CIT 0.0002015 0.41543 4.91803
173 2FWP ICR 0.0005168 0.40904 4.91803
174 2OFE NAG 0.0147 0.41779 4.92958
175 1G7V PAI 0.0004443 0.41595 4.92958
176 1Y2W NAG 0.02626 0.40599 4.92958
177 4Q3S X7A 0.0009692 0.4069 4.93506
178 1MXI SAH 0.003984 0.402 5
179 3Q3C NAD 0.0004655 0.42763 5.01672
180 2HNK SAH 0.001796 0.4105 5.02092
181 2GGH NLQ 0.000007391 0.42289 5.06667
182 2F59 INI 0.00186 0.41378 5.09554
183 1F8F NAD 0.0009973 0.4188 5.12129
184 4M5P 23W 0.00647 0.44741 5.15971
185 2NLI FMN 0.00002562 0.46558 5.16304
186 2NLI LAC 0.00002562 0.46558 5.16304
187 4GQP B40 0.01719 0.4028 5.22088
188 2TOH HBI 0.00005459 0.41603 5.24781
189 1H8G CHT 0.01376 0.45414 5.26316
190 3NGU ADP 0.001688 0.42801 5.29801
191 3HU3 AGS 0.004234 0.40302 5.31697
192 1EDO NAP 0.00004224 0.4734 5.32787
193 3CF6 SP1 0.001814 0.42238 5.38922
194 1JCM 137 0.00004867 0.42994 5.40541
195 3TO7 COA 0.00005134 0.44303 5.43478
196 2JE7 XMM 0.00004874 0.42353 5.43933
197 1I2B UPG 0.00002919 0.50523 5.44554
198 1I2B USQ 0.00002919 0.50523 5.44554
199 1I2B NAD 0.00002919 0.50523 5.44554
200 2ET1 GLV 0.0000007822 0.43622 5.47264
201 3QP4 HL0 0.004313 0.40825 5.49451
202 1N9L FMN 0.001724 0.41495 5.50459
203 2HMT NAI 0.00001239 0.47327 5.55556
204 2C1Q BTN 0.00003647 0.44885 5.55556
205 2QLX RM4 0.03313 0.40624 5.55556
206 2BZ1 TAU 0.0125 0.45652 5.61225
207 2BJK NAD 0.001645 0.4106 5.62015
208 3HPF GAE 0.00001151 0.42174 5.6266
209 2Y7G AAE 0.006518 0.40151 5.67376
210 3LTW HLZ 0.007955 0.43023 5.71429
211 3H86 AP5 0.0005562 0.42562 5.72917
212 4DN8 BMA 0.001735 0.46096 5.76923
213 2X61 NGA GAL SIA 0.00001809 0.47659 5.81395
214 2X61 CH 0.00002901 0.45187 5.81395
215 3S9K CIT 0.01306 0.45583 5.9322
216 4FR3 0V4 0.0007232 0.43314 5.98291
217 4FR3 LYS ARG ARG LYS SEP VAL 0.002076 0.41789 5.98291
218 1B4P GPS 0.002471 0.40938 5.99078
219 1FW1 GSH 0.005104 0.40947 6.01852
220 1WL4 COA 0.0003261 0.42457 6.04534
221 1X1T NAD 0.00005917 0.4701 6.15385
222 1UW1 ADP 0.004037 0.4379 6.25
223 4EKV BTN 0.000002713 0.47335 6.28931
224 3I51 45C 0.01077 0.40076 6.2963
225 2WLT ASP 0.0003291 0.40616 6.3253
226 3U1T MLI 0.01969 0.41725 6.47249
227 3I0O SMI 0.00723 0.42653 6.48968
228 3I0O ADP 0.009365 0.40731 6.48968
229 4FUA PGH 0.0003587 0.41169 6.51163
230 3NJQ NJQ 0.00001979 0.44942 6.73575
231 1Q3Q ANP 0.000005073 0.49439 6.75182
232 1Y9Q MED 0.004614 0.44123 6.77083
233 1U5R ATP 0.0007795 0.43613 6.89655
234 3GJB AKG 0.006615 0.41808 6.89655
235 1OFH ADP 0.002324 0.40933 6.89655
236 2BOI MFU 0.01694 0.40517 7.07965
237 1O9U ADZ 0.004651 0.46239 7.42857
238 1RSD PSB 0.02096 0.41186 7.43802
239 1V1A ADP 0.0001589 0.41522 7.44337
240 1V1A KDG 0.00005197 0.40575 7.44337
241 1W6M GAL 0.004238 0.40212 7.46269
242 3R51 MMA 0.01167 0.44156 7.5
243 4N02 FNR 0.0002648 0.43543 7.56302
244 3KMT SAH 0.007934 0.40206 7.56302
245 4F8L GAL 0.01783 0.44769 7.58621
246 2W3L DRO 0.01749 0.43236 7.63889
247 1WVC CTP 0.0002893 0.45369 7.72201
248 3L02 SN0 0.000104 0.40795 7.79944
249 3L02 CP 0.000104 0.40795 7.79944
250 1F5F DHT 0.004787 0.40276 7.80488
251 4AP9 1PS 0.00001453 0.41907 7.9602
252 3VGL BGC 0.000007886 0.45259 8.09969
253 3GIQ G01 0.0006079 0.4295 8.125
254 2Z9V PXM 0.02196 0.40023 8.16327
255 3VOZ 04A 0.0005502 0.43708 8.25397
256 2VAR AMP 0.004572 0.42006 8.30671
257 3QDY A2G GAL 0.01219 0.43361 8.39161
258 3QDY CBS 0.0216 0.41529 8.39161
259 3QDT A2G GAL 0.04969 0.40275 8.39161
260 2F2U M77 0.007975 0.41017 8.45771
261 2HVK TBA 0.000005916 0.5754 8.49057
262 4MWV BCZ 0.00003505 0.44664 8.50515
263 2YLD CMO 0.01609 0.41596 8.66142
264 1ULE GLA GAL NAG 0.02298 0.41975 8.66667
265 1ONX ASP 0.000001267 0.48521 8.71795
266 1YBQ BDH 0.00001708 0.41804 8.71795
267 4K30 NLG 0.008393 0.41849 8.75
268 1WKL ADP 0.0002913 0.44241 8.75912
269 1WKL ATP 0.000972 0.4238 8.75912
270 1NVU GTP 0.00001064 0.48198 9.03614
271 2BNE U5P 0.0006995 0.40319 9.12863
272 2GJ3 FAD 0.00004309 0.43404 9.16667
273 3NFZ 3NF 0.005111 0.41364 9.17431
274 1GSA ADP 0.0000004848 0.5174 9.17722
275 1GSA GSH 0.00001998 0.45945 9.17722
276 1T0S BML 0.003071 0.46359 9.30233
277 1T26 GBD 0.004225 0.41794 9.31677
278 1T26 NAI 0.004225 0.41794 9.31677
279 43CA NPO 0.0188 0.44638 9.40171
280 4DA6 GA2 0.0002946 0.43577 9.48617
281 1TUV VK3 0.0134 0.43842 9.64912
282 2BGM NAJ 0.0004134 0.43277 9.71223
283 4NTX AMR 0.008848 0.41999 10
284 1Y75 NAG 0.005213 0.42245 10.1695
285 1JQ5 NAD 0.001868 0.44172 10.2703
286 2ZO9 MLI 0.00004092 0.50018 10.5839
287 4HZD COA 0.000619 0.40671 10.6383
288 1XE7 GUN 0.01524 0.4355 10.8374
289 3F81 STT 0.04233 0.41214 10.929
290 2QCX PF1 0.007695 0.42531 11.0266
291 3K37 BCZ 0.0002645 0.45116 11.0831
292 4LKK SIA GAL 0.0001381 0.45393 11.1465
293 1OGD RIP 0.01643 0.40576 11.4504
294 1EXB NDP 0.0002 0.45245 12.6214
295 3BY8 MLT 0.03041 0.40805 12.6761
296 4UBP HAE 0.0113 0.4005 12.6984
297 3MAG 3MA 0.008337 0.45733 12.7036
298 4GQB 0XU 0.00001574 0.47444 13.6364
299 4IAE 1DX 0.000272 0.43268 13.7566
300 1NU4 MLA 0.01206 0.4218 14.433
301 3SJ0 DXC 0.0444 0.4 15.493
302 3RF4 FUN 0.013 0.41019 15.5172
303 3M0J OAF 0.00003768 0.43656 15.6352
304 2E1A MSE 0.005679 0.42088 17.3333
305 3EJ0 11X 0.00123 0.45785 17.8571
306 1QD0 RR6 0.00293 0.42323 17.9688
307 1FWE HAE 0.002419 0.43499 20.7547
308 3ZZS TRP 0.00005435 0.4381 23.0769
309 4C6F DOR 0.000000962 0.57754 39.6947
310 4C6F NCD 0.00001466 0.52188 39.6947
311 2FVK DUC 0.00000000001132 0.85974 49.4231
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