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Receptor
PDB id Resolution Class Description Source Keywords
3KVY 2.3 Å EC: 2.-.-.- TRAPPING OF AN OXOCARBENIUM ION INTERMEDIATE IN UP CRYSTALS BOS TAURUS OXOCARBENIUM ION GLYCAL PYRIMIDINE SALVAGE URIDINE PHOSPHTRANSFERASE
Ref.: GLYCAL FORMATION IN CRYSTALS OF URIDINE PHOSPHORYLA BIOCHEMISTRY V. 49 3499 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
R2B A:313;
B:313;
Valid;
Valid;
none;
none;
submit data
132.115 C5 H8 O4 C1=C(...
SO4 A:310;
A:311;
B:310;
B:311;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
URA A:312;
B:312;
Valid;
Valid;
none;
none;
submit data
112.087 C4 H4 N2 O2 C1=CN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3KVY 2.3 Å EC: 2.-.-.- TRAPPING OF AN OXOCARBENIUM ION INTERMEDIATE IN UP CRYSTALS BOS TAURUS OXOCARBENIUM ION GLYCAL PYRIMIDINE SALVAGE URIDINE PHOSPHTRANSFERASE
Ref.: GLYCAL FORMATION IN CRYSTALS OF URIDINE PHOSPHORYLA BIOCHEMISTRY V. 49 3499 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 269 families.
1 3KVY - URA C4 H4 N2 O2 C1=CNC(=O)....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 237 families.
1 3P0E - BAU C14 H16 N2 O4 c1ccc(cc1)....
2 3P0F - BAU C14 H16 N2 O4 c1ccc(cc1)....
3 3EUF - BAU C14 H16 N2 O4 c1ccc(cc1)....
4 3NBQ - URF C4 H3 F N2 O2 C1=C(C(=O)....
5 3KVY - URA C4 H4 N2 O2 C1=CNC(=O)....
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3P0E - BAU C14 H16 N2 O4 c1ccc(cc1)....
2 3P0F - BAU C14 H16 N2 O4 c1ccc(cc1)....
3 3EUF - BAU C14 H16 N2 O4 c1ccc(cc1)....
4 3NBQ - URF C4 H3 F N2 O2 C1=C(C(=O)....
5 5CYF - FLC C6 H5 O7 C(C(=O)[O-....
6 4TXJ - THM C10 H14 N2 O5 CC1=CN(C(=....
7 4TXM - TDR C5 H6 N2 O2 CC1=CNC(=O....
8 4TXL - URA C4 H4 N2 O2 C1=CNC(=O)....
9 4TXN - URF C4 H3 F N2 O2 C1=C(C(=O)....
10 3KVY - URA C4 H4 N2 O2 C1=CNC(=O)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: R2B; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 R2B 1 1
2 LCN 0.575758 0.875
Ligand no: 2; Ligand: URA; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 URA 1 1
2 TUL 0.5 0.725
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3KVY; Ligand: R2B; Similar sites found with APoc: 70
This union binding pocket(no: 1) in the query (biounit: 3kvy.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 5EWK P34 None
2 1CT9 GLN 1.61812
3 5Z5I XYS 1.94175
4 5Z5I FUB 1.94175
5 5UY8 AMZ 1.94175
6 4PIO AVI 1.94175
7 1H74 ADP 2.02703
8 2A8Y MTA 2.22222
9 1U2Z SAH 2.26537
10 1MXH NAP 2.53623
11 1MXH DHF 2.53623
12 4GQB 0XU 2.589
13 4QIJ 1HA 2.589
14 1ZOS MTM 2.6087
15 4IZC 1GZ 2.90909
16 1NJJ ORX 2.91262
17 1N46 PFA 3.10078
18 2G2Y MLI 3.24675
19 2PHN GDP 3.54331
20 4K38 SAM 3.55987
21 3UB7 ACM 3.8674
22 5U3F 7TS 3.8835
23 1VFS DCS 3.8835
24 2OO0 PLP 3.8835
25 4IXH IMP 4.20712
26 1NY5 ADP 4.20712
27 2JBM SRT 4.53074
28 3BL6 FMC 4.78261
29 1YQS BSA 5.17799
30 6GNF QPS 5.17799
31 1NB9 ADP 5.44218
32 1NB9 RBF 5.44218
33 5M7P ADP 5.50162
34 3DZD ADP 5.50162
35 4Y9J FAD 5.82524
36 6AYR BIG 5.88235
37 4Z87 5GP 6.14887
38 1E7S NAP 6.14887
39 4HXY NDP 6.47249
40 3KOX Z98 6.61157
41 4QAR ADE 6.96517
42 5F7J ADE 7.1875
43 5XWV NDP 7.44337
44 3GBR PRP 7.44337
45 4WKC BIG 7.7551
46 4FFS BIG 8.3682
47 4BMX ADE 9.56175
48 1NW4 IMH 10.1449
49 1K27 MTM 10.2473
50 2NVA PL2 10.356
51 2AC7 ADN 10.6383
52 3RUV ANP 12.6214
53 3LGS ADE 14.2322
54 3LGS SAH 14.2322
55 6F4W FMC 16.7382
56 5FAG PPI 16.8285
57 2V92 ATP 18.3908
58 4WKB TDI 23.3607
59 3QPB R1P 24.8227
60 4DA6 GA2 29.249
61 3BJE R1P 30.4207
62 3BJE URA 30.4207
63 1JE1 GMP 31.7797
64 1Z34 2FD 33.1915
65 4YJK URA 33.3333
66 1U1F 183 33.9844
67 3U40 ADN 34.2975
68 1A69 FMB 34.874
69 1VHW ADN 38.7352
70 1ODJ GMP 39.1489
Pocket No.: 2; Query (leader) PDB : 3KVY; Ligand: R2B; Similar sites found with APoc: 13
This union binding pocket(no: 2) in the query (biounit: 3kvy.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 4PIO SAH 1.94175
2 4GK9 MAN BMA MAN MAN MAN 2.86738
3 5ZQS BXP 2.91262
4 4I4Z 2NE 3.27273
5 6H1U ASP 3.48432
6 3X0V FAD 3.55987
7 1P4A PCP 4.21053
8 2VZ0 D64 4.85075
9 2VZ0 NAP 4.85075
10 3WCA FPS 6.47249
11 5XWV 8H6 7.44337
12 3GDN MXN 8.73786
13 3QPB URA 24.8227
Pocket No.: 3; Query (leader) PDB : 3KVY; Ligand: URA; Similar sites found with APoc: 220
This union binding pocket(no: 3) in the query (biounit: 3kvy.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 5AHW CMP None
2 5EWK P34 None
3 3EFV NAD 0.970874
4 1SMR PIV HIS PRO PHE HIS LPL TYR TYR SER 1.2945
5 3KYG 5GP 5GP 1.32159
6 2JAJ D20 1.38408
7 4B2Z P5S 1.61812
8 1EFY BZC 1.61812
9 3ZOK NAD 1.61812
10 3PDB PMP 1.61812
11 3PD6 PMP 1.61812
12 3ITJ FAD 1.77515
13 1RJW ETF 1.94175
14 6GWR FEW 1.94175
15 3L4S NAD 1.94175
16 3L4S 3PG 1.94175
17 4IY7 KOU 1.94175
18 3KJS NAP 1.94175
19 5MJI 7O6 1.94553
20 2YBQ UP2 2.05479
21 1VKF CIT 2.12766
22 5NB7 8NQ 2.17391
23 1OG1 TAD 2.21239
24 2A8Y MTA 2.22222
25 5K3W PLP 2.26537
26 1T90 NAD 2.26537
27 1PJS SAH 2.26537
28 1DL5 SAH 2.26537
29 5WAN FMN 2.26537
30 1JGT CMA 2.26537
31 1JGT APC 2.26537
32 6CEP NAD 2.26537
33 4NMC FAD 2.26537
34 1U2Z SAH 2.26537
35 4X1B MLI 2.26537
36 3G6K POP 2.27273
37 3G6K FAD 2.27273
38 2NXE SAM 2.3622
39 5AAV GW5 2.38095
40 2BJ4 OHT 2.38095
41 2RDE C2E 2.39044
42 3G89 SAM 2.40964
43 3DAA PDD 2.52708
44 5MDH NAD 2.589
45 5W5R PYR 2.589
46 4MDH NAD 2.589
47 1GAD NAD 2.589
48 5N5S NAP 2.589
49 1ZOS MTM 2.6087
50 2WSI FAD 2.61438
51 4FK7 P34 2.62009
52 5BV6 35G 2.63158
53 3SLS ANP 2.63158
54 5ZW3 SAH 2.66667
55 6MPT C30 2.7972
56 1IYE PGU 2.91262
57 3DLG GWE 2.91262
58 3VPH NAD 2.91262
59 3VPH OXM 2.91262
60 1V7C HEY 2.91262
61 5AHM IMP 2.91262
62 1D1G NDP 2.97619
63 1Q2C COA 3.08642
64 2I0G I0G 3.11284
65 4YDD MD1 3.23625
66 4YDD MGD 3.23625
67 3OV6 MK0 3.23625
68 3VC3 C6P 3.23625
69 2C5S AMP 3.23625
70 4K33 ACP 3.23625
71 2E2R 2OH 3.27869
72 1CX9 NHP 3.35821
73 1SR7 MOF 3.4749
74 4OAR 2S0 3.48837
75 6AM8 PLT 3.55987
76 6AM8 TRP 3.55987
77 1TDF FAD 3.55987
78 6AMI TRP 3.55987
79 4M3P HCS 3.55987
80 4A62 ANP 3.55987
81 4R2M ANP 3.79747
82 2P4S DIH 3.8835
83 5U3F 7TS 3.8835
84 2XZ9 PYR 3.8835
85 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 3.8835
86 3HXU A5A 3.8835
87 4A2A ATP 3.8835
88 1XXR MAN 3.8835
89 3ZF8 GDP 3.93443
90 4OFG PCG 4.16667
91 2C78 PUL 4.20712
92 1GQG DCD 4.20712
93 5W75 SUC 4.20712
94 4IXH IMP 4.20712
95 2FK8 SAM 4.20712
96 1X7D ORN 4.20712
97 1KC7 PPR 4.20712
98 1G55 SAH 4.20712
99 3C3N FMN 4.20712
100 1TT8 PHB 4.26829
101 2F6U CIT 4.2735
102 1HDR NAD 4.5082
103 4NKW PLO 4.53074
104 3RLF ANP 4.53074
105 4XCB HY0 4.5977
106 1ZY5 ANP 4.62046
107 4X6F 3XU 4.62633
108 1NHZ 486 4.64286
109 2IVF MGD 4.6729
110 3BL6 FMC 4.78261
111 1I2L DCS 4.83271
112 5G0H E1Z 4.85437
113 1Q3Q ANP 4.92701
114 2FLI DX5 5
115 4KQ6 DLZ 5.02793
116 3OQJ 3CX 5.05837
117 4KCT PYR 5.17799
118 5GXU FMN 5.17799
119 4CE5 PDG 5.40541
120 5X8G S0N 5.50162
121 4DP3 NDP 5.50162
122 4DP3 MMV 5.50162
123 2J8Z NAP 5.50162
124 4MSG 2C6 5.52995
125 2G37 FAD 5.82524
126 5UC1 486 5.85586
127 6AYR BIG 5.88235
128 6C7Y ADP 5.98291
129 4LAE NAP 5.98802
130 4LAE 1VM 5.98802
131 3KMZ EQO 6.01504
132 2XXP DSL 6.03015
133 4GLJ RHB 6.06061
134 3HGM ATP 6.12245
135 1VMK GUN 6.13718
136 4Z87 5GP 6.14887
137 6ES0 BW8 6.14887
138 3CF6 SP1 6.14887
139 4Z0G 5GP 6.14887
140 1MJH ATP 6.17284
141 1QL9 ZEN 6.27803
142 1B8O IMH 6.33803
143 5M42 FMN 6.45161
144 5ETJ IM5 6.47249
145 4ZOH MCN 6.54762
146 1PZG A3D 6.79612
147 2BW7 ECS 6.84932
148 2A5F NAD 6.85714
149 4QAR ADE 6.96517
150 2AX9 BHM 7.03125
151 5F7J ADE 7.1875
152 3UZO PLP 7.44337
153 3UZO GLU 7.44337
154 4WKC BIG 7.7551
155 5IFK HPA 7.76699
156 5C5H 4YB 7.76699
157 4XTX 590 7.77778
158 3CBG SAH 8.09062
159 1KYV RBF 8.1761
160 4K2G 1OQ 8.23529
161 5F7N NAG GAL FUC FUC A2G 8.33333
162 5F7Y GLC GAL NAG GAL FUC A2G 8.33333
163 3DJF BC3 8.36237
164 4FFS BIG 8.3682
165 4UUG PXG 8.41424
166 2A0W DIH 8.65052
167 2A9K NAD 8.96861
168 2E7Z MGD 9.06149
169 2C6Q IMP 9.06149
170 2HKJ RDC 9.06149
171 3SHR CMP 9.36455
172 1GZF NIR 9.47867
173 1GZF NAD 9.47867
174 4BMX ADE 9.56175
175 5LD5 NAD 9.70874
176 1NW4 IMH 10.1449
177 1K27 MTM 10.2473
178 6B5G NAD 10.356
179 2AC7 ADN 10.6383
180 4NG2 OHN 10.8696
181 1HDG NAD 11.0032
182 3HQP OXL 11.0032
183 4XSH NAI 11.1732
184 5YSI NCA 11.1842
185 4WVO 3UZ 11.3269
186 4KM2 TOP 11.7318
187 4KM2 ATR 11.7318
188 1G2O IMH 11.9403
189 1AJQ SPA 11.9617
190 1U1B PAX 12.0968
191 3PG7 PTY 12.1094
192 5DXV NAP 12.1795
193 4PZ2 NAD 12.2977
194 4RT1 C2E 13.3929
195 3DUW SAH 13.4529
196 6ACS CIT 13.5659
197 3LGS ADE 14.2322
198 3LGS SAH 14.2322
199 5Y4R C2E 14.966
200 3VSE SAH 15.5779
201 1B1C FMN 16.5746
202 5TBS ADE 16.7247
203 6F4W FMC 16.7382
204 4M7V NAP 17.1429
205 5KY3 GFB 17.5
206 6C5F 7L9 18.8034
207 5JAX 6J7 19.2593
208 1MUU NAD 22.3301
209 4WKB TDI 23.3607
210 3QPB URA 24.8227
211 4DA6 GA2 29.249
212 3BJE URA 30.4207
213 1JE1 GMP 31.7797
214 1Z34 2FD 33.1915
215 4YJK URA 33.3333
216 1U1F 183 33.9844
217 3U40 ADN 34.2975
218 1A69 FMB 34.874
219 1VHW ADN 38.7352
220 1ODJ GMP 39.1489
Pocket No.: 4; Query (leader) PDB : 3KVY; Ligand: URA; Similar sites found with APoc: 31
This union binding pocket(no: 4) in the query (biounit: 3kvy.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 5DX1 SFG 1.61812
2 4PJT 2YQ 1.62162
3 4OXX FMN 1.85185
4 5EK3 5PK 1.94175
5 4BVA T3 1.94175
6 6BHV DQV 2.21402
7 5WS9 AMP 2.26537
8 2VYN NAD 2.26537
9 2AMT GPP 2.51572
10 5FUB SAH 2.589
11 2OYS FMN 2.89256
12 2JCB ADP 2.91262
13 5UKL SIX 3.23625
14 4PAB THG 3.23625
15 1E5Q SHR 3.23625
16 2EW5 Y12 3.31492
17 2GFD RDA 3.38983
18 4OR7 NAP 3.63636
19 4ONA UW1 3.8835
20 3KJD 78P 3.8835
21 1Z4O GL1 4.0724
22 3X0D SAH 5.17799
23 3MPI GRA 5.50162
24 3WYJ H78 5.92885
25 4MIB 28M 6.47249
26 1MGP PLM 6.47249
27 4YC0 5OF 7.11974
28 3IA4 NDP 8.64198
29 4UTG ANP 10.0324
30 4M73 SAH 10.6796
31 4M73 M72 10.6796
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