Receptor
PDB id Resolution Class Description Source Keywords
2HRM 1.7 Å EC: 3.6.1.23 CRYSTAL STRUCTURE OF DUTPASE COMPLEXED WITH SUBSTRATE ANALOG METHYLENE-DUTP ESCHERICHIA COLI JELLY ROLL ENZYME-SUBSTRATE ANALOGUE LIGAND COMPLEX HYDROL
Ref.: METHYLENE SUBSTITUTION AT THE ALPHA-BETA BRIDGING P WITHIN THE PHOSPHATE CHAIN OF DUDP PROFOUNDLY PERTU LIGAND ACCOMMODATION INTO THE DUTPASE ACTIVE SITE. PROTEINS V. 71 308 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:301;
Invalid;
none;
submit data
62.068 C2 H6 O2 C(CO)...
UC5 A:777;
Valid;
none;
Kd = 287.5 uM
386.189 C10 H16 N2 O10 P2 C1[C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1RN8 1.93 Å EC: 3.6.1.23 CRYSTAL STRUCTURE OF DUTPASE COMPLEXED WITH SUBSTRATE ANALOGUE IMIDO-DUTP ESCHERICHIA COLI JELLY ROLL ENZYME-LIGAND COMPLEX HYDROLASE
Ref.: STRUCTURAL INSIGHTS INTO THE CATALYTIC MECHANISM OF PHOSPHATE ESTER HYDROLYSIS BY DUTPASE. J.BIOL.CHEM. V. 279 42907 2004
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 1SEH - UMP C9 H13 N2 O8 P C1[C@@H]([....
2 1DUD Ki = 15 uM DUD C9 H14 N2 O11 P2 C1[C@@H]([....
3 1SYL - DUT C9 H15 N2 O14 P3 C1[C@@H]([....
4 1RN8 Kd = 1 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
5 1RNJ - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
6 2HR6 Kd = 12 uM DUD C9 H14 N2 O11 P2 C1[C@@H]([....
7 2HRM Kd = 287.5 uM UC5 C10 H16 N2 O10 P2 C1[C@@H]([....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 1SEH - UMP C9 H13 N2 O8 P C1[C@@H]([....
2 1DUD Ki = 15 uM DUD C9 H14 N2 O11 P2 C1[C@@H]([....
3 1SYL - DUT C9 H15 N2 O14 P3 C1[C@@H]([....
4 1RN8 Kd = 1 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
5 1RNJ - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
6 2HR6 Kd = 12 uM DUD C9 H14 N2 O11 P2 C1[C@@H]([....
7 2HRM Kd = 287.5 uM UC5 C10 H16 N2 O10 P2 C1[C@@H]([....
50% Homology Family (26)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 181 families.
1 5NYZ - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
2 5CCO - UMP C9 H13 N2 O8 P C1[C@@H]([....
3 5CCT - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
4 4GV8 Kd = 0.32 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
5 3EHW - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
6 2HQU Kd = 1.6 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
7 3ARA ic50 = 0.32 uM MKH C24 H27 N3 O5 S c1ccc(cc1)....
8 3ARN ic50 = 3.9 uM MSJ C17 H23 N3 O5 S CC(C)(CCCO....
9 3P48 - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
10 1Q5H - DUD C9 H14 N2 O11 P2 C1[C@@H]([....
11 4OOP - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
12 1F7P - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
13 3F4F - UMP C9 H13 N2 O8 P C1[C@@H]([....
14 1DUC - DUD C9 H14 N2 O11 P2 C1[C@@H]([....
15 1SEH - UMP C9 H13 N2 O8 P C1[C@@H]([....
16 1DUD Ki = 15 uM DUD C9 H14 N2 O11 P2 C1[C@@H]([....
17 1SYL - DUT C9 H15 N2 O14 P3 C1[C@@H]([....
18 2HR6 Kd = 12 uM DUD C9 H14 N2 O11 P2 C1[C@@H]([....
19 2HRM Kd = 287.5 uM UC5 C10 H16 N2 O10 P2 C1[C@@H]([....
20 2OL0 - DUD C9 H14 N2 O11 P2 C1[C@@H]([....
21 2OKE - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
22 2OL1 - UMP C9 H13 N2 O8 P C1[C@@H]([....
23 3H6D - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
24 3HZA - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
25 3LOJ - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
26 1SMC - DUT C9 H15 N2 O14 P3 C1[C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: UC5; Similar ligands found: 40
No: Ligand ECFP6 Tc MDL keys Tc
1 UC5 1 1
2 DU 0.772727 0.970588
3 UMP 0.772727 0.970588
4 DUD 0.71831 0.985294
5 DUN 0.69863 0.957143
6 DUT 0.68 0.985294
7 DUP 0.671053 0.957143
8 DUT MG 0.662338 0.888889
9 DUS 0.642857 0.831169
10 UMP AF3 PO4 0.632911 0.853333
11 DUR 0.606061 0.855072
12 44P 0.573333 0.942857
13 UM3 0.52 0.927536
14 DDN 0.506494 0.970588
15 DU DU DU DU BRU DU DU 0.490196 0.842105
16 DDU 0.485714 0.732394
17 DU3 0.45977 0.783784
18 DUA 0.45977 0.786667
19 UFP 0.45679 0.90411
20 U5P 0.455696 0.885714
21 BRU 0.451219 0.90411
22 5HU 0.451219 0.943662
23 TMP 0.451219 0.929577
24 DU4 0.449438 0.74026
25 5IU 0.445783 0.90411
26 UDP 0.440476 0.9
27 DCM 0.433735 0.902778
28 DC 0.433735 0.902778
29 UTP 0.425287 0.9
30 TYD 0.425287 0.943662
31 Y6W 0.416667 0.878378
32 BVP 0.41573 0.916667
33 UNP 0.411111 0.875
34 YYY 0.409091 0.916667
35 UDX 0.408163 0.875
36 UAD 0.408163 0.875
37 UDP UDP 0.406977 0.84507
38 TTP 0.406593 0.943662
39 2KH 0.404494 0.875
40 UPU 0.402174 0.847222
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1RN8; Ligand: DUP; Similar sites found: 67
This union binding pocket(no: 1) in the query (biounit: 1rn8.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1SS4 GSH 0.00432 0.47926 None
2 1LO8 4CA 0.002234 0.42514 None
3 2Q37 3AL 0.005592 0.42493 None
4 4JB1 FAD 0.02952 0.41637 None
5 4JB1 NAP 0.03316 0.41297 None
6 3ZZL TRP 0.002592 0.40556 None
7 1C1L GAL BGC 0.01393 0.41829 1.45985
8 3H86 AP5 0.0009382 0.43261 1.97368
9 1H6W SER LEU ASN TYR ILE ILE LYS VAL LYS GLU 0.002084 0.41792 1.97368
10 3S9K CIT 0.001731 0.51244 2.54237
11 3Q3C NAD 0.0003086 0.44906 2.63158
12 1PEA ACM 0.02634 0.41078 2.63158
13 1D7O TCL 0.01238 0.40758 2.63158
14 1D7O NAD 0.01238 0.40758 2.63158
15 1V6A TRE 0.001607 0.44875 3.28947
16 1SAY PYR 0.005616 0.43353 3.28947
17 1A5Z NAD 0.002588 0.41334 3.28947
18 1RYI FAD 0.00329 0.40414 3.28947
19 1RM4 NDP 0.00904 0.40202 3.28947
20 4F4S EFO 0.003495 0.42824 3.94737
21 4IAE 1DX 0.001534 0.42254 3.94737
22 4Q0P 0MK 0.008334 0.41891 3.94737
23 1TV5 ORO 0.00373 0.40187 3.94737
24 1Z44 NPO 0.002098 0.49367 4.60526
25 4OYA 1VE 0.004822 0.42979 4.60526
26 2OWZ F6P 0.001086 0.41821 4.60526
27 3K37 BCZ 0.007871 0.41278 4.60526
28 1HV9 COA 0.002762 0.41237 4.60526
29 1KGQ SCO 0.01006 0.40884 4.60526
30 3ZPG 5GP 0.04748 0.40376 4.60526
31 3MB5 SAM 0.006297 0.40164 4.60526
32 1EXB NDP 0.002745 0.42724 5.26316
33 1I2B UPG 0.01049 0.424 5.26316
34 1I2B USQ 0.01049 0.424 5.26316
35 1I2B NAD 0.01049 0.424 5.26316
36 1GR0 NAD 0.009184 0.40919 5.26316
37 1JQ5 NAD 0.02003 0.41428 5.92105
38 2X61 CH 0.001435 0.41415 5.92105
39 2ZO9 MLI 0.004039 0.4132 5.92105
40 1NXJ TLA 0.0000668 0.40603 5.92105
41 1RP0 AHZ 0.003275 0.42319 6.57895
42 3L8W XAN 0.003765 0.41414 6.57895
43 3HRD FAD 0.03586 0.40637 6.57895
44 1PJ6 FOL 0.003699 0.40436 6.57895
45 2WR8 SAH 0.002308 0.40273 7.23684
46 3FS8 ACO 0.0208 0.40011 7.23684
47 2HMT NAI 0.001829 0.41856 7.63889
48 3KPE TM3 0.001542 0.4562 7.69231
49 1KY8 NAP 0.009922 0.4151 7.89474
50 2IMP NAI 0.0116 0.4076 7.89474
51 2IMP LAC 0.0002643 0.40329 7.89474
52 1T3Q FAD 0.01423 0.42324 8.55263
53 3F81 STT 0.03146 0.41306 8.55263
54 4E28 9MZ 0.009614 0.42001 9.21053
55 1FFU FAD 0.01811 0.41692 9.21053
56 4E28 0MZ 0.01619 0.40457 9.21053
57 2P4T NAP 0.001526 0.40346 9.67742
58 1E8G FCR 0.01594 0.40728 11.1842
59 1E8G FAD 0.01683 0.40728 11.1842
60 4IZC 1GZ 0.002285 0.41653 14.4737
61 1V5F FAD 0.006418 0.43797 16.4474
62 1V5F TPP 0.006418 0.43797 16.4474
63 1OFH ADP 0.005029 0.41041 17.1053
64 2R0N TGC 0.02895 0.40658 21.0526
65 1F8F NAD 0.002335 0.41993 25
66 2QXX TTP 0.0006255 0.47061 31.5789
67 1XS1 DUT 0.003904 0.43082 43.4211
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