Receptor
PDB id Resolution Class Description Source Keywords
2PY4 1.49 Å EC: 3.6.1.23 FULL LENGTH STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS DUTP COMPLEXED WITH MAGNESIUM AND ALPHA,BETA-IMIDO-DUTP. MYCOBACTERIUM TUBERCULOSIS JELLY-ROLL ENZYME-LIGAND COMPLEX HYDROLASE
Ref.: ACTIVE SITE OF MYCOBACTERIAL DUTPASE: STRUCTURAL CHARACTERISTICS AND A BUILT-IN SENSOR. BIOCHEM.BIOPHYS.RES.COMMUN. V. 373 8 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DUP A:777;
Valid;
none;
Kd = 0.2 uM
467.157 C9 H16 N3 O13 P3 C1[C@...
TRS A:201;
Invalid;
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
2PY4 1.49 Å EC: 3.6.1.23 FULL LENGTH STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS DUTP COMPLEXED WITH MAGNESIUM AND ALPHA,BETA-IMIDO-DUTP. MYCOBACTERIUM TUBERCULOSIS JELLY-ROLL ENZYME-LIGAND COMPLEX HYDROLASE
Ref.: ACTIVE SITE OF MYCOBACTERIAL DUTPASE: STRUCTURAL CHARACTERISTICS AND A BUILT-IN SENSOR. BIOCHEM.BIOPHYS.RES.COMMUN. V. 373 8 2008
Members (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 3I93 - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
2 3H6D - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
3 3HZA - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
4 5EDD Kd = 5.7 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
5 1SIX - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
6 5ECT Kd = 5.2 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
7 2PY4 Kd = 0.2 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
8 1SNF - UMP C9 H13 N2 O8 P C1[C@@H]([....
9 3LOJ - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
10 1SMC - DUT C9 H15 N2 O14 P3 C1[C@@H]([....
70% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 1SJN - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
2 3I93 - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
3 3H6D - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
4 3HZA - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
5 5EDD Kd = 5.7 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
6 1SIX - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
7 5ECT Kd = 5.2 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
8 2PY4 Kd = 0.2 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
9 1SNF - UMP C9 H13 N2 O8 P C1[C@@H]([....
10 3LOJ - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
11 1SMC - DUT C9 H15 N2 O14 P3 C1[C@@H]([....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 1SJN - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
2 1RN8 Kd = 1 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
3 1RNJ - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
4 3I93 - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
5 5EDD Kd = 5.7 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
6 1SIX - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
7 5ECT Kd = 5.2 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
8 2PY4 Kd = 0.2 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
9 1SNF - UMP C9 H13 N2 O8 P C1[C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DUP; Similar ligands found: 35
No: Ligand ECFP6 Tc MDL keys Tc
1 DUP 1 1
2 DUN 0.816901 1
3 DU 0.742857 0.956522
4 UMP 0.742857 0.956522
5 DUD 0.739726 0.971014
6 DUT 0.701299 0.971014
7 UC5 0.671053 0.957143
8 DUT MG 0.621951 0.876712
9 DUS 0.6 0.820513
10 UMP AF3 PO4 0.595238 0.842105
11 DUR 0.585714 0.842857
12 2KH 0.585366 0.915493
13 UM3 0.506329 0.914286
14 DU DU DU DU BRU DU DU 0.495238 0.831169
15 DDN 0.47561 0.956522
16 DU4 0.472527 0.730769
17 BRU 0.458824 0.891892
18 DDU 0.453333 0.722222
19 DUA 0.450549 0.776316
20 DU3 0.450549 0.773333
21 TYD 0.449438 0.930556
22 UFP 0.447059 0.891892
23 5HU 0.44186 0.930556
24 TMP 0.44186 0.916667
25 5IU 0.436782 0.891892
26 UNP 0.434783 0.915493
27 YYY 0.433333 0.90411
28 UDP 0.431818 0.887324
29 TTP 0.430108 0.930556
30 DC 0.425287 0.890411
31 DCM 0.425287 0.890411
32 UTP 0.417582 0.887324
33 DCP 0.414894 0.90411
34 U5P 0.411765 0.873239
35 BVP 0.408602 0.90411
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2PY4; Ligand: DUP; Similar sites found: 76
This union binding pocket(no: 1) in the query (biounit: 2py4.bio1) has 44 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1GXU 2HP 0.001511 0.47359 None
2 1BTN I3P 0.04086 0.44306 None
3 2VKL MLT 0.03172 0.43647 None
4 1XPJ TLA 0.02289 0.40941 None
5 3EJ0 11X 0.03162 0.40627 1.14943
6 1V6A TRE 0.006788 0.43981 1.72414
7 5A2J ALA PRO ASP THR ARG PRO 0.03014 0.42771 1.72414
8 4DN8 BMA 0.0008229 0.48963 1.92308
9 1XX4 BAM 0.001262 0.47068 2.29885
10 2ZJ5 ADP 0.04436 0.40147 2.29885
11 3MAG 3MA 0.02678 0.44065 2.87356
12 2Q8H TF4 0.02493 0.43535 2.87356
13 2O66 FLC 0.003746 0.45187 2.96296
14 3E81 SLB 0.03955 0.40384 3.04878
15 1NU4 MLA 0.01921 0.44881 3.09278
16 2JK0 ASP 0.0382 0.40515 3.38462
17 2ZWS PLM 0.00114 0.52912 3.44828
18 4PPU TYR 0.007945 0.43146 3.44828
19 1O9U ADZ 0.03606 0.42662 3.44828
20 4COQ SAN 0.02072 0.42203 3.44828
21 3K3G MMU 0.02137 0.41416 3.44828
22 2OG2 MLI 0.01918 0.41185 3.44828
23 4WVH ASP HIS ASP ALA HIS ALA 0.01735 0.41171 3.44828
24 4IXW IXW 0.02796 0.40254 3.44828
25 1TUV VK3 0.01102 0.45454 3.50877
26 4RJK PYR 0.01936 0.45691 4.02299
27 4B9E FAH 0.02888 0.42011 4.02299
28 1GPJ CIT 0.04013 0.40801 4.02299
29 3NOJ PYR 0.0005053 0.4889 4.5977
30 4MOB ADP 0.00606 0.41298 4.5977
31 3GTD MLI 0.03373 0.40712 4.5977
32 4EXO PYR 0.02096 0.43298 4.79452
33 3BRE C2E 0.04295 0.40656 5.17241
34 3R51 MMA 0.005287 0.47173 5.625
35 4K30 NLG 0.01688 0.40817 5.625
36 3E5P PPI 0.01122 0.48051 6.32184
37 2NZ2 ASP 0.001421 0.46526 6.32184
38 2AWN ADP 0.03032 0.412 6.32184
39 4NTX AMR 0.03324 0.40526 6.72269
40 1DXY COI 0.02681 0.43363 6.89655
41 2YLD CMO 0.02389 0.41902 6.89655
42 1JN2 SFP 0.0008043 0.54765 7.47126
43 4M7F BM3 0.0008313 0.47577 7.47126
44 1W3R PYR 0.02011 0.43391 7.47126
45 4WBD CIT 0.02485 0.42912 7.47126
46 1SC3 MLI 0.01577 0.43942 8.04598
47 1GJW GLC 0.01498 0.43446 8.04598
48 3W5J GDP 0.04145 0.40404 8.04598
49 3VCA PRO 0.007212 0.43593 8.62069
50 2OBM ADP 0.03221 0.41101 8.62069
51 1SS4 CIT 0.004685 0.52173 9.15033
52 1SS4 GSH 0.02716 0.45427 9.15033
53 4M5P MLA 0.007445 0.47199 9.1954
54 4M5P 23W 0.03629 0.42049 9.1954
55 2BZ1 TAU 0.01611 0.46162 9.69388
56 3QDY A2G GAL 0.009608 0.4506 9.77011
57 3QDT A2G GAL 0.01778 0.4367 9.77011
58 3QDY CBS 0.03254 0.41749 9.77011
59 1H0C AOA 0.04444 0.41062 9.77011
60 1YOA FMN 0.0009055 0.53499 10.3448
61 2HVK TBA 0.0007136 0.49261 10.4839
62 4E28 0MZ 0.02742 0.41138 12.069
63 2BO4 FLC 0.02121 0.42687 12.6437
64 1WKL ADP 0.001672 0.42853 13.1387
65 3PLN U5P 0.02548 0.40845 13.2184
66 4IHQ ADP 0.02316 0.40617 13.2184
67 2Q28 ADP 0.004681 0.4084 14.3678
68 5DRN 5CT 0.03308 0.43195 15.814
69 2NCD ADP 0.01998 0.41785 16.092
70 1Y1A GSH 0.009317 0.48525 16.6667
71 1Y2W NAG 0.02075 0.422 17.6056
72 1O51 ADP 0.002705 0.40097 18.4211
73 3S9K CIT 0.00116 0.54881 19.4915
74 1OGD RIP 0.007683 0.43212 19.8473
75 2QXX TTP 0.0004972 0.44884 24.1379
76 3KPE TM3 0.0003354 0.50838 43.1373
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