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Receptor
PDB id Resolution Class Description Source Keywords
2QCD 2.03 Å EC: 4.1.1.23 CRYSTAL STRUCTURE OF THE OROTIDINE-5'-MONOPHOSPHATE DECARBOX DOMAIN OF HUMAN UMP SYNTHASE BOUND TO UMP HOMO SAPIENS UMP SYNTHASE DECARBOXYLASE CATALYTIC PROFICIENCY LYASE
Ref.: STRUCTURES OF THE HUMAN OROTIDINE-5'-MONOPHOSPHATE DECARBOXYLASE SUPPORT A COVALENT MECHANISM AND PROV FRAMEWORK FOR DRUG DESIGN. STRUCTURE V. 16 82 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
U5P A:1;
B:2;
Valid;
Valid;
none;
none;
submit data
324.181 C9 H13 N2 O9 P C1=CN...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2QCD 2.03 Å EC: 4.1.1.23 CRYSTAL STRUCTURE OF THE OROTIDINE-5'-MONOPHOSPHATE DECARBOX DOMAIN OF HUMAN UMP SYNTHASE BOUND TO UMP HOMO SAPIENS UMP SYNTHASE DECARBOXYLASE CATALYTIC PROFICIENCY LYASE
Ref.: STRUCTURES OF THE HUMAN OROTIDINE-5'-MONOPHOSPHATE DECARBOXYLASE SUPPORT A COVALENT MECHANISM AND PROV FRAMEWORK FOR DRUG DESIGN. STRUCTURE V. 16 82 2008
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 2QCD - U5P C9 H13 N2 O9 P C1=CN(C(=O....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 2QCD - U5P C9 H13 N2 O9 P C1=CN(C(=O....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2QCD - U5P C9 H13 N2 O9 P C1=CN(C(=O....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: U5P; Similar ligands found: 121
No: Ligand ECFP6 Tc MDL keys Tc
1 U 1 1
2 U5P 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 UDP UDP 0.727273 0.953846
8 UPU 0.694444 0.954545
9 UNP 0.690141 0.955224
10 660 0.662338 0.913043
11 URM 0.662338 0.913043
12 URI 0.661017 0.848485
13 GUD 0.641026 0.926471
14 UFM 0.641026 0.926471
15 UPG 0.641026 0.926471
16 GDU 0.641026 0.926471
17 UPF 0.6375 0.875
18 U2F 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 CJB 0.603175 0.80597
24 UDX 0.597561 0.926471
25 UAD 0.597561 0.926471
26 3UC 0.588235 0.875
27 U U 0.585366 0.969697
28 UGB 0.583333 0.940298
29 USQ 0.583333 0.807692
30 UGA 0.583333 0.940298
31 5FU 0.57971 0.927536
32 G3N 0.576471 0.9
33 UA3 0.573529 0.953846
34 U3P 0.573529 0.953846
35 CAR 0.571429 0.941176
36 C 0.571429 0.941176
37 C5P 0.571429 0.941176
38 UDM 0.568182 0.9
39 5BU 0.56338 0.927536
40 U4S 0.557143 0.763889
41 UD1 0.555556 0.913043
42 UD2 0.555556 0.913043
43 CSQ 0.550562 0.863014
44 CSV 0.550562 0.863014
45 U2S 0.541667 0.777778
46 U3S 0.541667 0.763889
47 CNU 0.540541 0.941176
48 S5P 0.535211 0.901408
49 16B 0.534247 0.901408
50 U2P 0.528571 0.939394
51 DU 0.527778 0.911765
52 UMP 0.527778 0.911765
53 HP7 0.526882 0.926471
54 UD7 0.526882 0.913043
55 MJZ 0.521277 0.9
56 UP6 0.521127 0.884058
57 12V 0.515789 0.887324
58 F5G 0.515789 0.913043
59 UD4 0.515789 0.9
60 HWU 0.515789 0.887324
61 F5P 0.515789 0.9
62 BMP 0.513889 0.955224
63 UP5 0.510204 0.84
64 DKX 0.507246 0.732394
65 NUP 0.506849 0.927536
66 U6M 0.506849 0.969697
67 IUG 0.505155 0.797468
68 EPZ 0.5 0.9
69 U1S 0.5 0.76
70 4TC 0.5 0.818182
71 JW5 0.5 0.955224
72 EEB 0.49505 0.887324
73 A U 0.49505 0.815789
74 EPU 0.49505 0.887324
75 UDZ 0.494949 0.84
76 H2U 0.486111 0.911765
77 OMP 0.480519 0.969697
78 6AU 0.480519 0.969697
79 6CN 0.480519 0.941176
80 TKW 0.48 0.927536
81 UMF 0.479452 0.869565
82 UUA 0.477612 0.757576
83 U U U U 0.476744 0.954545
84 BMQ 0.472222 0.939394
85 PUP 0.47191 0.926471
86 G U 0.471154 0.797468
87 5HM 0.467532 0.888889
88 O7E 0.463415 0.941176
89 ICR 0.460526 0.830986
90 UMA 0.458716 0.9
91 O7M 0.45679 0.941176
92 UC5 0.455696 0.885714
93 UTP U U U 0.454545 0.909091
94 CDP 0.45 0.927536
95 2TU 0.449275 0.760563
96 FNU 0.441558 0.876712
97 2QR 0.439655 0.810127
98 DUD 0.4375 0.898551
99 N3E 0.4375 0.743243
100 2OM 0.435897 0.925373
101 U21 0.434783 0.797468
102 U20 0.434783 0.797468
103 U22 0.434783 0.777778
104 DUT 0.433735 0.898551
105 HF4 0.433735 0.927536
106 CTP 0.433735 0.927536
107 8OP 0.428571 0.849315
108 8GM 0.421687 0.853333
109 5GW 0.420455 0.927536
110 U A A U 0.418803 0.853333
111 4RA 0.414634 0.842105
112 DUP 0.411765 0.873239
113 DUN 0.409639 0.873239
114 UD0 0.408 0.831169
115 UVC 0.407895 0.842857
116 UM3 0.407895 0.897059
117 C5G 0.404255 0.875
118 UPA 0.401869 0.828947
119 A U C C 0.401639 0.794872
120 UAG 0.4 0.851351
121 A G U 0.4 0.7875
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2QCD; Ligand: U5P; Similar sites found with APoc: 189
This union binding pocket(no: 1) in the query (biounit: 2qcd.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 3BW2 FMN 1.15385
3 1PZ1 NAP 1.15385
4 2B4B B33 1.16959
5 2DUR MAN MAN 1.18577
6 4PZ6 GMP 1.53846
7 2BTM PGA 1.5873
8 1ICP FMN 1.92308
9 4TMC FMN 1.92308
10 1LBF 137 2.02429
11 4UTW RFW 2.18341
12 4UTU LRY 2.18341
13 3N9R TD3 2.30769
14 5C9P FUC 2.30769
15 5OPJ AHR 2.30769
16 4ETZ C2E 2.30769
17 2Q3R FMN 2.30769
18 3GD8 GOL 2.69058
19 1GVF PGH 2.69231
20 2FJK 13P 2.69231
21 4ORM FMN 2.69231
22 4ORM 2V6 2.69231
23 4ORM ORO 2.69231
24 3CHT 4NB 2.69231
25 4RW3 IPD 2.69231
26 3HF3 FMN 2.69231
27 5XG5 A2G 2.75862
28 1B09 PC 2.91262
29 2O66 FLC 2.96296
30 3MMH SME 2.99401
31 1OX5 1PR 3.07692
32 1FDJ 13P 3.07692
33 1PVN MZP 3.07692
34 1ME8 RVP 3.07692
35 4IXH IMP 3.07692
36 4LUT DCS 3.07692
37 3GAY P6T 3.07692
38 1QPR PPC 3.07692
39 1OYB HBA 3.25
40 1OYB FMN 3.25
41 5J5R 6G1 3.3419
42 5J5R IMP 3.3419
43 2F6U CIT 3.4188
44 4Q4K FMN 3.46154
45 4Z87 5GP 3.46154
46 4Z0G 5GP 3.46154
47 2WL9 MBD 3.46154
48 3CV6 HXS 3.46154
49 3CV6 NAP 3.46154
50 3WQD PLP 999 3.46154
51 5T79 NDP 3.46154
52 3OVR 5SP 3.50877
53 3KDN CAP 3.84615
54 3GLC R5P 3.84615
55 4QNW FMN 3.84615
56 1PS9 FMN 3.84615
57 3VKC FPQ 3.84615
58 2BLE 5GP 3.84615
59 5AHN IMP 3.84615
60 2C6Q NDP 3.84615
61 2G50 PYR 3.84615
62 1JCM 137 3.861
63 1QDS PGA 3.98406
64 2W5P CL8 4.02685
65 6BVE PGA 4.08163
66 2Y88 2ER 4.09836
67 4XH0 ADP 4.23077
68 4V15 PLP 4.23077
69 2HSA FMN 4.23077
70 3ZGJ RMN 4.23077
71 3WG6 NDP 4.23077
72 4HDK 13X 4.23077
73 2OEM 1AE 4.23077
74 4RQL SNE 4.23077
75 4YMZ 13P 4.38247
76 4NAE 1GP 4.44444
77 2V63 CAP 4.61538
78 1VKF CIT 4.61538
79 2V6A CAP 4.61538
80 2VDH CAP 4.61538
81 2V67 CAP 4.61538
82 2V68 CAP 4.61538
83 5NXX 3Q7 4.61538
84 5OCS FMN 4.61538
85 2Q3O FMN 4.61538
86 4BI7 PGA 4.66926
87 1UZH CAP 4.91803
88 3B0P FMN 5
89 1Z44 FMN 5
90 3KRU FMN 5
91 1Z48 FMN 5
92 4KCT PYR 5
93 1Z42 FMN 5
94 2EV9 SKM 5
95 2Z6J FMN 5
96 1Z41 FMN 5
97 3SAO DBH 5
98 3FIU POP 5.22088
99 2YPI PGA 5.26316
100 1M5W DXP 5.34979
101 1RBL CAP 5.38462
102 5YSN 5AD 5.38462
103 3NZ1 3NY 5.38462
104 5A5W GUO 5.5336
105 4EWN 0VR 5.5336
106 1TRD PGH 5.6
107 1LYX PGA 5.64516
108 5CSS G3P 5.75221
109 2AWN ADP 5.76923
110 3W9Z FMN 5.76923
111 3UWV 2PG 5.76923
112 5GVH FMN 5.76923
113 3VSV XYP 5.76923
114 5BRP PNG 5.76923
115 5YJS SAL 5.76923
116 1C1L GAL BGC 5.83942
117 4KAX 4IP 5.91716
118 1W8S FBP 6.15385
119 1KBI PYR 6.15385
120 1KBI FMN 6.15385
121 1KBJ FMN 6.15385
122 4A3U FMN 6.15385
123 4LOO SB4 6.15385
124 4IGH 1EA 6.15385
125 4IGH FMN 6.15385
126 4IGH ORO 6.15385
127 1UUO BRF 6.15385
128 1UUO FMN 6.15385
129 1UUO ORO 6.15385
130 2FKA BEF 6.20155
131 1Y7P RIP 6.27803
132 3EXS 5RP 6.33484
133 5EYW PGA 6.4257
134 3CTL S6P 6.49351
135 4YVN EBS 6.53846
136 6GWR FEW 6.53846
137 5HJQ I3P 6.53846
138 1UZD CAP 6.71642
139 1SW0 PGA 6.85484
140 6BKA FMN 6.92308
141 4RJK PYR 6.92308
142 1V59 NAD 6.92308
143 1Q6O LG6 6.94444
144 1CKM GTP 7.30769
145 4TO8 FLC 7.30769
146 2VD9 EPC 7.30769
147 2VD9 IN5 7.30769
148 4JEJ 1GP 8.19672
149 5TCI MLI 8.33333
150 3N75 G4P 8.46154
151 2FLI DX5 8.63636
152 3TAO PGH 8.84615
153 3QH2 3NM 9.04977
154 4IP7 FLC 9.23077
155 2R14 TXD 9.23077
156 2R14 FMN 9.23077
157 4A59 AMP 9.23077
158 2GJN NIS 9.23077
159 1VYP TNF 9.23077
160 1CX9 NHP 9.32836
161 2ZRU FMN 9.61539
162 2C5S AMP 9.61539
163 1YNQ NDP 9.61539
164 1UJP CIT 10
165 1IR2 CAP 10
166 5HWV MBN 10
167 2TPS TPS 10.1322
168 4JIQ FMN 10.3846
169 4JIQ 1L5 10.3846
170 5N9Z CAP 10.7914
171 5HX1 UMP 10.8696
172 5F90 GLA GAL BGC 5VQ 10.8974
173 1HSL HIS 10.9244
174 5U97 PIT 11.1538
175 2OO0 PLP 11.5385
176 2HJ4 PNZ 11.9231
177 1I7M PUT 11.9403
178 1L5Y BEF 12.2581
179 6GMR F4K 12.3711
180 4TR9 38D 12.6923
181 4AF0 IMP 12.6923
182 5GJO PLP 13.4615
183 1TUF AZ1 13.4615
184 2ZI8 SDT 13.8462
185 4I9A NCN 14.6154
186 3ATY FMN 15
187 3DZ6 PUT 16.4179
188 1WDD CAP 25.7812
189 2FFC U5P 30.7692
Pocket No.: 2; Query (leader) PDB : 2QCD; Ligand: U5P; Similar sites found with APoc: 35
This union binding pocket(no: 2) in the query (biounit: 2qcd.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 2GOU FMN 1.15385
2 2RDT 2RD 1.92308
3 2RDT FMN 1.92308
4 4GNC ASO 2.30769
5 5XFV FMN 2.30769
6 2R5A MLZ 2.30769
7 3C3N FMN 2.30769
8 4AVV CD 2.45098
9 4AVV GHE 2.45098
10 4XP7 FNR 2.69231
11 5DQ8 FLF 2.91667
12 4M5P FMN 3.46154
13 1C1D PHE 3.46154
14 5WS9 OXL 3.46154
15 3O94 NCA 3.79147
16 1OVD FMN 3.84615
17 1OVD ORO 3.84615
18 5T9C G3P 3.84615
19 3U6W KIV 4.23077
20 3JQA DX4 4.23077
21 4Q0P 0MK 4.23077
22 43CA NPO 4.42478
23 4DNJ ANN 4.61538
24 2X8S AHR AHR AHR 4.61538
25 2Z6I FMN 5
26 1W6M GAL 5.22388
27 2EAE LBT 5.38462
28 5BXA MAN 5.76923
29 6GN6 GLC 5.76923
30 5KJW 53C 6.15385
31 1ST0 GTG 6.15385
32 1NIU DCS 6.53846
33 1OFD FMN 7.30769
34 3HYK A3P 7.37705
35 1VYP FMN 9.23077
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