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: 120
No: Ligand ECFP6 Tc MDL keys Tc
1 U5P 1 1
2 44P 0.790323 0.941176
3 UDP 0.78125 0.984615
4 UTP 0.746269 0.984615
5 2KH 0.735294 0.955224
6 UDP UDP 0.727273 0.953846
7 UPU 0.694444 0.954545
8 UNP 0.690141 0.955224
9 URM 0.662338 0.913043
10 660 0.662338 0.913043
11 URI 0.661017 0.848485
12 U 0.661017 0.848485
13 UFM 0.641026 0.926471
14 GDU 0.641026 0.926471
15 UPG 0.641026 0.926471
16 GUD 0.641026 0.926471
17 U2F 0.6375 0.875
18 UPF 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 UDP GAL 0.597561 0.898551
27 3UC 0.588235 0.875
28 U U 0.585366 0.969697
29 UGB 0.583333 0.940298
30 USQ 0.583333 0.807692
31 UGA 0.583333 0.940298
32 5FU 0.57971 0.927536
33 G3N 0.576471 0.9
34 U3P 0.573529 0.953846
35 UA3 0.573529 0.953846
36 C 0.571429 0.941176
37 CH 0.571429 0.926471
38 CAR 0.571429 0.941176
39 C5P 0.571429 0.941176
40 UDM 0.568182 0.9
41 5BU 0.56338 0.927536
42 U4S 0.557143 0.763889
43 UD1 0.555556 0.913043
44 UD2 0.555556 0.913043
45 CSQ 0.550562 0.863014
46 CSV 0.550562 0.863014
47 U3S 0.541667 0.763889
48 U2S 0.541667 0.777778
49 CNU 0.540541 0.941176
50 S5P 0.535211 0.901408
51 16B 0.534247 0.901408
52 U2P 0.528571 0.939394
53 DU 0.527778 0.911765
54 UMP 0.527778 0.911765
55 HP7 0.526882 0.926471
56 UD7 0.526882 0.913043
57 MJZ 0.521277 0.9
58 UP6 0.521127 0.884058
59 UD4 0.515789 0.9
60 HWU 0.515789 0.887324
61 12V 0.515789 0.887324
62 BMP 0.513889 0.955224
63 UP5 0.510204 0.84
64 DKX 0.507246 0.732394
65 U6M 0.506849 0.969697
66 NUP 0.506849 0.927536
67 IUG 0.505155 0.797468
68 EPZ 0.5 0.9
69 U1S 0.5 0.76
70 JW5 0.5 0.955224
71 4TC 0.5 0.818182
72 EPU 0.49505 0.887324
73 A U 0.49505 0.815789
74 EEB 0.49505 0.887324
75 UDZ 0.494949 0.84
76 H2U 0.486111 0.911765
77 6AU 0.480519 0.969697
78 OMP 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 5HM 0.467532 0.888889
87 O7E 0.463415 0.941176
88 ICR 0.460526 0.830986
89 UMA 0.458716 0.9
90 O7M 0.45679 0.941176
91 UC5 0.455696 0.885714
92 UTP U U U 0.454545 0.909091
93 CDP 0.45 0.927536
94 2TU 0.449275 0.760563
95 FNU 0.441558 0.876712
96 2QR 0.439655 0.810127
97 N3E 0.4375 0.743243
98 DUD 0.4375 0.898551
99 2OM 0.435897 0.925373
100 U22 0.434783 0.777778
101 U21 0.434783 0.797468
102 U20 0.434783 0.797468
103 DUT 0.433735 0.898551
104 CTP 0.433735 0.927536
105 8OP 0.428571 0.849315
106 8GM 0.421687 0.853333
107 5GW 0.420455 0.927536
108 U A A U 0.418803 0.853333
109 4RA 0.414634 0.842105
110 DUP 0.411765 0.873239
111 DUN 0.409639 0.873239
112 CDP MG 0.409639 0.861111
113 UD0 0.408 0.831169
114 UVC 0.407895 0.842857
115 UM3 0.407895 0.897059
116 C5G 0.404255 0.875
117 UPA 0.401869 0.828947
118 A U C C 0.401639 0.794872
119 A G U 0.4 0.7875
120 UAG 0.4 0.851351
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2QCD; Ligand: U5P; Similar sites found: 104
This union binding pocket(no: 1) in the query (biounit: 2qcd.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1PZ1 NAP 0.007649 0.40671 1.15385
2 2B4B B33 0.01061 0.42461 1.16959
3 2BTM PGA 0.001728 0.45604 1.5873
4 1ICP FMN 0.005387 0.41619 1.92308
5 4UTU LRY 0.0001191 0.49464 2.18341
6 4UTW RFW 0.0001366 0.45392 2.18341
7 4ETZ C2E 0.01906 0.40351 2.30769
8 2Q3R FMN 0.00565 0.40268 2.30769
9 1GVF PGH 0.002169 0.45668 2.69231
10 4ORM 2V6 0.02381 0.41384 2.69231
11 4ORM FMN 0.02381 0.41384 2.69231
12 4ORM ORO 0.02381 0.41384 2.69231
13 2FJK 13P 0.01359 0.4072 2.69231
14 4RW3 IPD 0.02018 0.4028 2.69231
15 3HF3 FMN 0.006408 0.40215 2.69231
16 4XP7 FNR 0.005027 0.40074 2.69231
17 3GAY P6T 0.00459 0.4065 3.07692
18 2F6U CIT 0.0001412 0.51723 3.4188
19 4Q4K FMN 0.001979 0.43083 3.46154
20 3WQD PLP 999 0.006213 0.40776 3.46154
21 3OVR 5SP 0.0003067 0.44254 3.50877
22 3KDN CAP 0.003223 0.44492 3.84615
23 3GLC R5P 0.003332 0.43222 3.84615
24 4QNW FMN 0.001643 0.41982 3.84615
25 1PS9 FMN 0.004201 0.41173 3.84615
26 3VKC FPQ 0.003161 0.40759 3.84615
27 2BLE 5GP 0.00842 0.40627 3.84615
28 1JCM 137 0.001284 0.42113 3.861
29 1QDS PGA 0.001698 0.45108 3.98406
30 2W5P CL8 0.02393 0.40412 4.02685
31 4XH0 ADP 0.004159 0.44414 4.23077
32 4V15 PLP 0.004661 0.42532 4.23077
33 3ZGJ RMN 0.009856 0.41837 4.23077
34 4YMZ 13P 0.002713 0.44629 4.38247
35 4NAE 1GP 0.0002266 0.51211 4.44444
36 1VKF CIT 0.008424 0.42466 4.61538
37 2V6A CAP 0.002022 0.42158 4.61538
38 2VDH CAP 0.001612 0.42018 4.61538
39 2V63 CAP 0.001633 0.41994 4.61538
40 2V68 CAP 0.002443 0.4181 4.61538
41 2V67 CAP 0.002256 0.4119 4.61538
42 2Q3O FMN 0.002139 0.40862 4.61538
43 4BI7 PGA 0.003254 0.44236 4.66926
44 1UZH CAP 0.002934 0.40963 4.91803
45 3B0P FMN 0.0004397 0.46338 5
46 3KRU FMN 0.002043 0.4389 5
47 1Z44 FMN 0.002256 0.43566 5
48 1Z41 FMN 0.002337 0.43063 5
49 4KCT PYR 0.00609 0.4288 5
50 1Z48 FMN 0.002597 0.42856 5
51 1Z42 FMN 0.008521 0.41289 5
52 3SAO DBH 0.01854 0.40143 5
53 3FIU POP 0.0239 0.40202 5.22088
54 2YPI PGA 0.001744 0.45053 5.26316
55 1M5W DXP 0.01049 0.42166 5.34979
56 1RBL CAP 0.0009633 0.43913 5.38462
57 5A5W GUO 0.0003042 0.48504 5.5336
58 4EWN 0VR 0.001974 0.43395 5.5336
59 1TRD PGH 0.001876 0.44403 5.6
60 1LYX PGA 0.001426 0.40824 5.64516
61 3W9Z FMN 0.001399 0.43227 5.76923
62 2AWN ADP 0.0146 0.42439 5.76923
63 5BRP PNG 0.02094 0.40466 5.76923
64 1C1L GAL BGC 0.02234 0.40053 5.83942
65 4LOO SB4 0.003419 0.41923 6.15385
66 1W8S FBP 0.006297 0.41504 6.15385
67 1KBJ FMN 0.005243 0.41241 6.15385
68 4A3U FMN 0.004994 0.40677 6.15385
69 4IGH ORO 0.04122 0.40276 6.15385
70 4IGH FMN 0.04122 0.40276 6.15385
71 4IGH 1EA 0.04122 0.40276 6.15385
72 2FKA BEF 0.007568 0.42088 6.20155
73 1Y7P RIP 0.02285 0.40224 6.27803
74 3EXS 5RP 0.00002891 0.53679 6.33484
75 5EYW PGA 0.001534 0.45861 6.4257
76 3CTL S6P 0.001265 0.43021 6.49351
77 4YVN EBS 0.02033 0.40814 6.53846
78 5HJQ I3P 0.0238 0.40058 6.53846
79 1UZD CAP 0.001907 0.42458 6.71642
80 1SW0 PGA 0.002113 0.44158 6.85484
81 4RJK PYR 0.01864 0.40892 6.92308
82 1Q6O LG6 0.000005415 0.51066 6.94444
83 1CKM GTP 0.01022 0.41759 7.30769
84 4TO8 FLC 0.004891 0.41636 7.30769
85 2VD9 IN5 0.005378 0.41427 7.30769
86 2VD9 EPC 0.007561 0.40398 7.30769
87 4JEJ 1GP 0.0004761 0.4722 8.19672
88 2FLI DX5 0.0001061 0.46775 8.63636
89 3QH2 3NM 0.0008527 0.47738 9.04977
90 4IP7 FLC 0.006241 0.43322 9.23077
91 2C5S AMP 0.02162 0.40129 9.61539
92 1UJP CIT 0.002755 0.42337 10
93 1IR2 CAP 0.002163 0.41472 10
94 4JIQ FMN 0.009799 0.40057 10.3846
95 5HX1 UMP 0.01653 0.41284 10.8696
96 2OO0 PLP 0.003908 0.42054 11.5385
97 1I7M PUT 0.02529 0.40052 11.9403
98 1L5Y BEF 0.001423 0.46454 12.2581
99 4AF0 IMP 0.004539 0.41029 12.6923
100 5GJO PLP 0.001097 0.41384 13.4615
101 4I9A NCN 0.008634 0.40143 14.6154
102 3DZ6 PUT 0.02919 0.40372 16.4179
103 1WDD CAP 0.002498 0.41769 25.7812
104 2FFC U5P 0.00000001918 0.64227 30.7692
Pocket No.: 2; Query (leader) PDB : 2QCD; Ligand: U5P; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2qcd.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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