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Receptor
PDB id Resolution Class Description Source Keywords
4OOP 1.5 Å EC: 3.6.1.23 ARABIDOPSIS THALIANA DUTPASE WITH WITH MAGNESIUM AND ALPHA,B DUTP ARABIDOPSIS THALIANA DUTPASE HYDROLYSIS DUTP HYDROLASE
Ref.: STRUCTURAL INSIGHTS INTO THE MECHANISM DEFINING SUB AFFINITY IN ARABIDOPSIS THALIANA DUTPASE: THE ROLE TRYPTOPHAN 93 IN LIGAND ORIENTATION. BMC RES NOTES V. 8 784 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:202;
C:201;
Invalid;
Invalid;
none;
none;
submit data
24.305 Mg [Mg+2...
DUP B:202;
B:203;
A:201;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
467.157 C9 H16 N3 O13 P3 C1[C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4OOP 1.5 Å EC: 3.6.1.23 ARABIDOPSIS THALIANA DUTPASE WITH WITH MAGNESIUM AND ALPHA,B DUTP ARABIDOPSIS THALIANA DUTPASE HYDROLYSIS DUTP HYDROLASE
Ref.: STRUCTURAL INSIGHTS INTO THE MECHANISM DEFINING SUB AFFINITY IN ARABIDOPSIS THALIANA DUTPASE: THE ROLE TRYPTOPHAN 93 IN LIGAND ORIENTATION. BMC RES NOTES V. 8 784 2015
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 4OOP - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 16 families.
1 4OOP - DUP C9 H16 N3 O13 P3 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 204 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 5H4J Ki = 0.13 uM FKM C21 H29 N3 O6 S C[C@H](c1c....
7 2HQU Kd = 1.6 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
8 3ARA ic50 = 0.32 uM MKH C24 H27 N3 O5 S c1ccc(cc1)....
9 3ARN ic50 = 3.9 uM MSJ C17 H23 N3 O5 S CC(C)(CCCO....
10 3P48 - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
11 1Q5H - DUD C9 H14 N2 O11 P2 C1[C@@H]([....
12 4OOP - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
13 1F7N - UMP C9 H13 N2 O8 P C1[C@@H]([....
14 1F7Q - DUT C9 H15 N2 O14 P3 C1[C@@H]([....
15 1F7P - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
16 3F4F - UMP C9 H13 N2 O8 P C1[C@@H]([....
17 1DUC - DUD C9 H14 N2 O11 P2 C1[C@@H]([....
18 1RN8 Kd = 1 uM DUP C9 H16 N3 O13 P3 C1[C@@H]([....
19 1RNJ - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
20 2HR6 Kd = 12 uM DUD C9 H14 N2 O11 P2 C1[C@@H]([....
21 2HRM Kd = 287.5 uM UC5 C10 H16 N2 O10 P2 C1[C@@H]([....
22 2OL0 - DUD C9 H14 N2 O11 P2 C1[C@@H]([....
23 2OKE - DUP C9 H16 N3 O13 P3 C1[C@@H]([....
24 2OL1 - UMP C9 H13 N2 O8 P 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: DUP; Similar ligands found: 34
No: Ligand ECFP6 Tc MDL keys Tc
1 DUP 1 1
2 DUN 0.816901 1
3 UMP 0.742857 0.956522
4 DU 0.742857 0.956522
5 DUD 0.739726 0.971014
6 DUT 0.701299 0.971014
7 UC5 0.671053 0.957143
8 DUS 0.6 0.820513
9 DUR 0.585714 0.842857
10 2KH 0.585366 0.915493
11 UM3 0.506329 0.914286
12 DU DU DU DU BRU DU DU 0.495238 0.831169
13 DDN 0.47561 0.956522
14 DU4 0.472527 0.730769
15 BRU 0.458824 0.891892
16 DDU 0.453333 0.722222
17 DUA 0.450549 0.776316
18 DU3 0.450549 0.773333
19 TYD 0.449438 0.930556
20 UFP 0.447059 0.891892
21 TMP 0.44186 0.916667
22 5HU 0.44186 0.930556
23 5IU 0.436782 0.891892
24 UNP 0.434783 0.915493
25 YYY 0.433333 0.90411
26 UDP 0.431818 0.887324
27 TTP 0.430108 0.930556
28 DC 0.425287 0.890411
29 DCM 0.425287 0.890411
30 UTP 0.417582 0.887324
31 DCP 0.414894 0.90411
32 U 0.411765 0.873239
33 U5P 0.411765 0.873239
34 BVP 0.408602 0.90411
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4OOP; Ligand: DUP; Similar sites found with APoc: 58
This union binding pocket(no: 1) in the query (biounit: 4oop.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 1ZEI CRS None
2 5N1P 8GK None
3 3KV8 FAH 2.15827
4 1PZM 5GP 2.40964
5 4B2D SER 3.01205
6 5NC9 8SZ 3.01205
7 2JBH 5GP 3.01205
8 3BP1 GUN 3.61446
9 1JXZ BCA 3.61446
10 2BL9 NDP 3.61446
11 2BL9 CP6 3.61446
12 3OND NAD 4.21687
13 3OND ADN 4.21687
14 3RNM FAD 4.21687
15 1KQN NAD 4.21687
16 4Z2S NDG 4.22535
17 4Z2S NAG 4.22535
18 2OFD NGA 4.22535
19 2OFE NAG 4.22535
20 4FGC PQ0 4.24242
21 5HJQ I3P 4.81928
22 3QDV NDG 4.8951
23 3QDY CBS 4.8951
24 3QDX CBS 4.8951
25 3QDW NDG 4.8951
26 3QDU CBS CBS 4.8951
27 2MBR EPU 5.42169
28 2UUU PL3 5.42169
29 2UUU FAD 5.42169
30 1NZY BCA 5.42169
31 4JLS 3ZE 5.92105
32 4JB1 NAP 6.0241
33 4JB1 FAD 6.0241
34 2WD7 VGD 6.0241
35 5M67 NAD 6.0241
36 5M67 3D1 6.0241
37 5M67 ADE 6.0241
38 2NU8 COA 6.0241
39 5H4S RAM 6.0241
40 5G5G FAD 6.62651
41 3W6G FLC 7.83133
42 2V2V V12 8.43373
43 4A59 AMP 8.43373
44 3HRD FAD 8.43373
45 3HRD NIO 8.43373
46 2HQM FAD 9.03614
47 3FXU TSU 10.8434
48 3W8X FTK 12.0482
49 3W8X FAD 12.0482
50 5JBX MLI 12.0482
51 1FFU FAD 12.6506
52 5Y6Q FAD 18.0723
53 1XS1 DUT 19.2771
54 4P86 5GP 19.8795
55 4XJC TTP 21.0843
56 4LAE NAP 30.7229
57 4LAE 1VM 30.7229
58 5Y5Q DUT 46.3855
Pocket No.: 2; Query (leader) PDB : 4OOP; Ligand: DUP; Similar sites found with APoc: 37
This union binding pocket(no: 2) in the query (biounit: 4oop.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 4CS9 AMP None
2 1MZV AMP 2.40964
3 1Y2W NAG 2.8169
4 3MAG SAH 3.01205
5 3MCT SAH 3.01205
6 2J9D ADP 3.36134
7 1OFD FMN 3.61446
8 1OFD AKG 3.61446
9 1L1Q 9DA 3.61446
10 4CZG QH3 3.61446
11 4CZG ADP 3.61446
12 6D6L FY4 3.61446
13 2F5Z FAD 4.21687
14 4P83 U5P 4.21687
15 1J3I NDP 4.21687
16 2JB2 FAD 4.21687
17 2JB2 PHE 4.21687
18 4YJI TYL 4.21687
19 1V84 GAL NDG 4.81928
20 1Q19 APC 4.81928
21 2ZXI FAD 4.81928
22 4IV9 FAD 4.81928
23 1L6O SER LEU LYS LEU MET THR THR VAL 5.26316
24 2MBR FAD 5.42169
25 2ZJ1 NAD 5.42169
26 2ZJ1 ARJ 5.42169
27 3JQA DX4 6.0241
28 5GVR LMR 6.0241
29 3QDL FMN 6.0241
30 5BVA FAD 6.62651
31 2WOX NDP 8.43373
32 1RM6 FAD 9.63855
33 2GMH FAD 12.0482
34 1UYY BGC BGC 12.9771
35 3JZ4 NAP 13.8554
36 1N62 FAD 22.2892
37 2QXX TTP 35.5422
Pocket No.: 3; Query (leader) PDB : 4OOP; Ligand: DUP; Similar sites found with APoc: 122
This union binding pocket(no: 3) in the query (biounit: 4oop.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 1GXU 2HP None
2 5H20 GLC None
3 5C2N NAG None
4 4U00 ADP 1.20482
5 1RL4 BRR 1.80723
6 3KO0 TFP 1.9802
7 2HPL ASP ASP LEU TYR GLY 2
8 4NOS H2B 2.40964
9 1B0U ATP 2.40964
10 4K6B GLU 2.48447
11 5EYW PGA 3.01205
12 5E9W SAH 3.01205
13 4RPM HXC 3.61446
14 1TL2 NDG 3.61446
15 4K30 NLG 3.75
16 2F6D ACR 4.21687
17 5TSH ADP 4.21687
18 4WZA ACP 4.21687
19 4WZA ADP 4.21687
20 1A0J BEN 4.21687
21 2G50 ALA 4.21687
22 3W5J GDP 4.21687
23 1C3X 8IG 4.21687
24 2HIM ASP 4.21687
25 1RRC ADP 4.21687
26 3B8I OXL 4.21687
27 2HIM ASN 4.21687
28 5F1V 3VN 4.81928
29 1Q19 SSC 4.81928
30 5FUS DAO 4.81928
31 6E8I PTR 4.81928
32 2PL3 ADP 4.81928
33 1QB7 ADE 4.81928
34 3FJG 3PG 4.81928
35 4EZD SEY 4.81928
36 2H5Z CTO 4.91803
37 5TQZ GLC 5.33333
38 1JJ7 ADP 5.42169
39 3B9Q MLI 5.42169
40 2ZUX RAM 5.42169
41 3AB4 THR 5.42169
42 1XPJ TLA 5.55556
43 4KJU 1RH 5.81395
44 3JUC PCA 5.88235
45 3E7S AT2 6.0241
46 4CU1 H4B 6.0241
47 5JCJ 6JM 6.0241
48 2CBZ ATP 6.0241
49 5JDI 6JO 6.0241
50 3B99 U51 6.0241
51 3BMN AX3 6.0241
52 5JDC 6JP 6.0241
53 5ZYN SIN 6.0241
54 4CME KTZ 6.0241
55 5C9P FUC 6.0241
56 5K6A 6QT 6.0241
57 1Q8S MAN MMA 6.0241
58 4IHQ ADP 6.0241
59 3A4M ADP 6.53846
60 2DVZ GLU 6.62651
61 2W58 ADP 6.62651
62 5H6S HDH 6.62651
63 1JOT GAL A2G 6.76692
64 1JAC AMG 6.76692
65 1UGW GAL 6.76692
66 1UGY GLA BGC 6.76692
67 1WS5 MMA 6.76692
68 4AKB GAL 6.76692
69 1WS4 GYP 6.76692
70 1UGY GLA GLC 6.76692
71 1KUJ MMA 6.76692
72 1WS4 AMG 6.76692
73 1TOQ AMG 6.76692
74 4P87 4NP 7.22892
75 2PZE ATP 7.22892
76 2D2F ADP 7.22892
77 4D0N GDP 7.22892
78 2X7I CIT 7.22892
79 3KIF GDL 7.54717
80 5A96 GTP 7.83133
81 2JK0 ASP 7.83133
82 3VCA PRO 7.83133
83 5LJW ANP 7.83133
84 4U8P UDP 7.83133
85 1XX6 ADP 7.83133
86 4X7R UDP 7.83133
87 4U8P FDA 7.83133
88 3PIJ FRU 8.43373
89 2AWN ADP 8.43373
90 6C0B MLI 8.43373
91 2J5V PCA 8.43373
92 1DKU AP2 9.03614
93 4G86 BNT 9.03614
94 2GKS ADP 9.03614
95 2F6U CIT 9.63855
96 2QV7 ADP 9.63855
97 5V8E CIT 9.63855
98 1QH5 GSH 10.8434
99 3LZW FAD 10.8434
100 3MBI HSX 10.8434
101 4GUS FAD 11.2903
102 4GUT FAD 11.2903
103 4HSU FAD 11.2903
104 5L3S G 11.4458
105 4YAC NAI 12.0482
106 1YXM ADE 12.0482
107 4Z7X 3CX 12.6506
108 2I80 G1L 13.253
109 2AJ4 GLA 13.253
110 4XFR CIT 13.253
111 5LX9 OLB 13.8554
112 1GPM CIT 13.8554
113 2KIN ADP 15
114 5MB4 NAG 15.6627
115 5TE1 7A2 17.4699
116 3BY9 SIN 18.0723
117 3RC3 ANP 18.6747
118 4DYG MES 19.2771
119 5E5U MLI 19.8795
120 1G6H ADP 22.8916
121 1B4B ARG 23.9437
122 1P0Z FLC 25.9542
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