Receptor
PDB id Resolution Class Description Source Keywords
6A46 2 Å EC: 3.1.11.2 STRUCTURE OF TREX2 IN COMPLEX WITH A NUCLEOTIDE (DCMP) MUS MUSCULUS EXONUCLEASE DEDDH EXONUCLEASE DNA BINDING PROTEIN
Ref.: STRUCTURAL INSIGHTS INTO THE DUPLEX DNA PROCESSING NUCLEIC ACIDS RES. V. 46 12166 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA B:305;
A:304;
B:304;
Part of Protein;
Invalid;
Invalid;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
DCM A:303;
B:301;
Valid;
Valid;
none;
none;
submit data
307.197 C9 H14 N3 O7 P C1[C@...
MG B:303;
B:302;
A:302;
A:301;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6A46 2 Å EC: 3.1.11.2 STRUCTURE OF TREX2 IN COMPLEX WITH A NUCLEOTIDE (DCMP) MUS MUSCULUS EXONUCLEASE DEDDH EXONUCLEASE DNA BINDING PROTEIN
Ref.: STRUCTURAL INSIGHTS INTO THE DUPLEX DNA PROCESSING NUCLEIC ACIDS RES. V. 46 12166 2018
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 6A46 - DCM C9 H14 N3 O7 P 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 4 families.
1 6A46 - DCM C9 H14 N3 O7 P C1[C@@H]([....
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3U3Y - DG DA DC DG n/a n/a
2 3U6F - DG DA DC DG n/a n/a
3 3B6O - TMP C10 H15 N2 O8 P CC1=CN(C(=....
4 2OA8 - DG DA DC DG n/a n/a
5 3B6P - TMP C10 H15 N2 O8 P CC1=CN(C(=....
6 2O4G - TMP C10 H15 N2 O8 P CC1=CN(C(=....
7 2IOC - D5M C10 H14 N5 O6 P c1nc(c2c(n....
8 6A46 - DCM C9 H14 N3 O7 P C1[C@@H]([....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: DCM; Similar ligands found: 52
No: Ligand ECFP6 Tc MDL keys Tc
1 DCM 1 1
2 DC 1 1
3 YYY 0.80597 0.985714
4 DCP 0.760563 0.985714
5 0KX 0.75 0.958333
6 DCP MG 0.702703 0.957143
7 DCZ 0.693548 0.833333
8 LDC 0.693548 0.833333
9 5CM 0.608108 0.958333
10 DU 0.561644 0.928571
11 UMP 0.561644 0.928571
12 C5P 0.540541 0.902778
13 CAR 0.540541 0.902778
14 DOC 0.540541 0.971429
15 C 0.540541 0.902778
16 DDN 0.527027 0.928571
17 BRU 0.506494 0.866667
18 TMP 0.506494 0.890411
19 UFP 0.493506 0.866667
20 5HU 0.487179 0.878378
21 5IU 0.481013 0.866667
22 CPA 0.480769 0.860759
23 BVP 0.464286 0.878378
24 CDP 0.463415 0.890411
25 DCT 0.458824 0.957747
26 DUD 0.451219 0.915493
27 CGP 0.449541 0.851852
28 C3P 0.448718 0.888889
29 C2P 0.448718 0.902778
30 CTP 0.447059 0.890411
31 HF4 0.447059 0.890411
32 GCQ 0.44186 0.878378
33 8OG 0.44186 0.873418
34 LTT 0.438356 0.780822
35 2TM 0.436782 0.905405
36 UC5 0.433735 0.902778
37 3TC 0.432432 0.77027
38 DUT 0.430233 0.915493
39 GTF 0.426966 0.878378
40 0RC 0.426966 0.868421
41 7XL 0.426966 0.866667
42 DUP 0.425287 0.890411
43 CTN 0.424658 0.756757
44 AR3 0.424658 0.756757
45 DUN 0.423529 0.890411
46 UMC 0.4125 0.875
47 CXY 0.412371 0.866667
48 CDP MG 0.411765 0.863014
49 GEO 0.407895 0.76
50 QBT 0.407407 0.863014
51 TYD 0.406977 0.878378
52 I5A 0.4 0.743243
Similar Ligands (3D)
Ligand no: 1; Ligand: DCM; Similar ligands found: 129
No: Ligand Similarity coefficient
1 U 0.9889
2 U5P 0.9664
3 UP6 0.9650
4 FDM 0.9588
5 BMP 0.9547
6 CH 0.9529
7 DUS 0.9516
8 FN5 0.9509
9 H2U 0.9494
10 NYM 0.9487
11 9L3 0.9462
12 PSU 0.9442
13 D4M 0.9409
14 NUP 0.9406
15 BMQ 0.9397
16 16B 0.9394
17 TKW 0.9362
18 5BU 0.9355
19 5FU 0.9355
20 D5M 0.9339
21 DA 0.9338
22 U4S 0.9295
23 DI 0.9284
24 U6M 0.9284
25 AMP 0.9270
26 AMZ 0.9270
27 PFU 0.9261
28 2DT 0.9256
29 IMP 0.9250
30 AIR 0.9239
31 FNU 0.9238
32 S5P 0.9235
33 C2R 0.9233
34 U2S 0.9193
35 LMS 0.9186
36 5HM 0.9167
37 QTJ 0.9157
38 AS 0.9151
39 T3S 0.9150
40 6CN 0.9141
41 U1S 0.9108
42 U3S 0.9108
43 8BR 0.9086
44 6MA 0.9082
45 GAR 0.9077
46 FMP 0.9050
47 IRP 0.9030
48 DGP 0.9027
49 DG 0.9027
50 6MZ 0.9015
51 CNU 0.8998
52 5QT 0.8991
53 5GP 0.8989
54 EO7 0.8985
55 AZU 0.8962
56 NMN 0.8961
57 NCN 0.8960
58 ATM 0.8938
59 CMP 0.8935
60 FT1 0.8934
61 G 0.8923
62 IRN 0.8918
63 6SY 0.8916
64 IGP 0.8914
65 2GE 0.8904
66 FT2 0.8888
67 71V 0.8888
68 VKE 0.8878
69 8OP 0.8873
70 3RC 0.8873
71 XMP 0.8869
72 PZB 0.8834
73 6PG 0.8833
74 DRM 0.8822
75 NEC 0.8822
76 N5O 0.8815
77 CC7 0.8803
78 43J 0.8799
79 TXS 0.8795
80 RP1 0.8781
81 QTV 0.8773
82 QTK 0.8769
83 IMU 0.8758
84 VIB 0.8751
85 SP1 0.8748
86 FB4 0.8747
87 6AU 0.8746
88 9RK 0.8744
89 FAI 0.8743
90 OMP 0.8741
91 JW5 0.8738
92 MTM 0.8727
93 HDU 0.8725
94 UDP 0.8724
95 27M 0.8718
96 MTE 0.8714
97 1CE 0.8709
98 MTA 0.8708
99 2T4 0.8699
100 O7E 0.8696
101 IWH 0.8693
102 MTH 0.8689
103 TCL 0.8685
104 FT3 0.8684
105 15I 0.8678
106 9XZ 0.8677
107 43F 0.8669
108 URI 0.8668
109 9MK 0.8665
110 DUR 0.8658
111 8GM 0.8646
112 4X2 0.8631
113 S0J 0.8622
114 W1G 0.8602
115 I22 0.8601
116 SIJ 0.8599
117 FX5 0.8595
118 FBP 0.8593
119 2OM 0.8593
120 EP4 0.8589
121 43G 0.8576
122 22T 0.8571
123 KU1 0.8569
124 THM 0.8551
125 DZJ 0.8551
126 L02 0.8546
127 S45 0.8543
128 AFP 0.8533
129 URD 0.8523
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6A46; Ligand: DCM; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 6a46.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 2IDO TMP 20.4819
2 2IDO TMP 20.4819
Pocket No.: 2; Query (leader) PDB : 6A46; Ligand: DCM; Similar sites found with APoc: 2
This union binding pocket(no: 2) in the query (biounit: 6a46.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 2IDO TMP 20.4819
2 2IDO TMP 20.4819
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