Receptor
PDB id Resolution Class Description Source Keywords
1SYL 1.95 Å EC: 3.6.1.23 CRYSTAL STRUCTURE OF INACTIVE MUTANT DUTPASE COMPLEXED WITH DUTP ESCHERICHIA COLI ENZYME-LIGAND COMPLEX JELLY ROLL HYDROLASE
Ref.: STRUCTURAL INSIGHTS INTO THE CATALYTIC MECHANISM OF PHOSPHATE ESTER HYDROLYSIS BY DUTPASE J.BIOL.CHEM. V. 279 42907 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DUT A:777;
Valid;
none;
submit data
468.142 C9 H15 N2 O14 P3 C1[C@...
MG A:997;
Invalid;
none;
submit data
24.305 Mg [Mg+2...
TRS A:501;
A:502;
Invalid;
Invalid;
none;
none;
submit data
122.143 C4 H12 N O3 C(C(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: DUT; Similar ligands found: 82
No: Ligand ECFP6 Tc MDL keys Tc
1 DUT 1 1
2 DUD 0.880597 1
3 DU 0.753623 0.985075
4 UMP 0.753623 0.985075
5 DUP 0.701299 0.971014
6 UC5 0.68 0.985294
7 DUN 0.662338 0.971014
8 TTP 0.62963 0.957143
9 DUT MG 0.62963 0.901408
10 DCP 0.609756 0.929577
11 DUS 0.608108 0.842105
12 UMP AF3 PO4 0.60241 0.864865
13 UTP 0.6 0.913043
14 DUR 0.594203 0.867647
15 TYD 0.542169 0.957143
16 6U4 0.532609 0.857143
17 UDP 0.52439 0.913043
18 YYY 0.52381 0.929577
19 UM3 0.512821 0.941176
20 8DG 0.5 0.8375
21 DU DU DU DU BRU DU DU 0.485714 0.853333
22 DDN 0.481481 0.985075
23 UFP 0.46988 0.916667
24 DAU 0.46 0.891892
25 DDU 0.459459 0.742857
26 UNP 0.455556 0.887324
27 TLO 0.453608 0.90411
28 TRH 0.45 0.891892
29 18T 0.45 0.891892
30 1JB 0.45 0.891892
31 UDX 0.44898 0.887324
32 UAD 0.44898 0.887324
33 5HU 0.447059 0.957143
34 BRU 0.447059 0.916667
35 TMP 0.447059 0.942857
36 0FX 0.446602 0.868421
37 DU4 0.445652 0.75
38 5IU 0.44186 0.916667
39 T3F 0.441176 0.868421
40 T3Q 0.441176 0.868421
41 DU3 0.43956 0.794521
42 DUA 0.43956 0.797297
43 DGT 0.438776 0.7875
44 139 0.438596 0.8125
45 UDH 0.4375 0.891892
46 T46 0.436893 0.891892
47 3R2 0.435644 0.88
48 TDX 0.435644 0.90411
49 U5P 0.433735 0.898551
50 UFM 0.43299 0.861111
51 GUD 0.43299 0.861111
52 UPG 0.43299 0.861111
53 GDU 0.43299 0.861111
54 MMF 0.432692 0.868421
55 DCM 0.430233 0.915493
56 DC 0.430233 0.915493
57 3YN 0.427184 0.891892
58 DWN 0.427184 0.868421
59 8GD 0.427083 0.8375
60 QDM 0.424528 0.857143
61 0N2 0.423077 0.857143
62 UPP 0.42268 0.861111
63 FNF 0.420561 0.88
64 1YF 0.420561 0.88
65 AKM 0.420561 0.848101
66 UPF 0.42 0.815789
67 UFG 0.42 0.815789
68 U2F 0.42 0.815789
69 660 0.418367 0.901408
70 URM 0.418367 0.901408
71 8DD 0.418367 0.844156
72 2KH 0.417582 0.887324
73 3UC 0.417476 0.815789
74 4TG 0.416667 0.88
75 UPU 0.414894 0.859155
76 D3T 0.413043 0.929577
77 BVP 0.413043 0.929577
78 PUA 0.409836 0.846154
79 G3N 0.407767 0.888889
80 JHZ 0.407407 0.846154
81 44P 0.402299 0.928571
82 T5A 0.401709 0.804878
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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