Receptor
PDB id Resolution Class Description Source Keywords
3B6O 2.1 Å EC: 3.1.11.2 STRUCTURE OF TREX1 IN COMPLEX WITH A NUCLEOTIDE AND AN INHIBITOR ION (LITHIUM) MUS MUSCULUS TREX1 DEDD EXONUCLEASE DNAQ LITHIUM CATALYSIS INHIBITION DEOXY-THIMIDINE MONOPHOSPHATE (DTMP) DNA DAMAGE DNA REPAIR HYDROLASE MAGNESIUM NUCLEUS PHOSPHORYLATION
Ref.: STRUCTURAL AND BIOCHEMICAL STUDIES OF TREX1 INHIBITION BY METALS. IDENTIFICATION OF A NEW ACTIVE HISTIDINE CONSERVED IN DEDDH EXONUCLEASES. PROTEIN SCI. V. 17 2059 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
LI A:800;
B:800;
C:800;
D:800;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
6.941 Li [Li+]
TMP A:1000;
B:1000;
C:1000;
D:1000;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
322.208 C10 H15 N2 O8 P CC1=C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3B6O 2.1 Å EC: 3.1.11.2 STRUCTURE OF TREX1 IN COMPLEX WITH A NUCLEOTIDE AND AN INHIBITOR ION (LITHIUM) MUS MUSCULUS TREX1 DEDD EXONUCLEASE DNAQ LITHIUM CATALYSIS INHIBITION DEOXY-THIMIDINE MONOPHOSPHATE (DTMP) DNA DAMAGE DNA REPAIR HYDROLASE MAGNESIUM NUCLEUS PHOSPHORYLATION
Ref.: STRUCTURAL AND BIOCHEMICAL STUDIES OF TREX1 INHIBITION BY METALS. IDENTIFICATION OF A NEW ACTIVE HISTIDINE CONSERVED IN DEDDH EXONUCLEASES. PROTEIN SCI. V. 17 2059 2008
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3B6O - TMP C10 H15 N2 O8 P CC1=CN(C(=....
2 2OA8 - DG DA DC DG n/a n/a
3 3B6P - TMP C10 H15 N2 O8 P CC1=CN(C(=....
4 2O4G - TMP C10 H15 N2 O8 P CC1=CN(C(=....
5 2IOC - D5M C10 H14 N5 O6 P c1nc(c2c(n....
70% Homology Family (7)
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....
50% Homology Family (7)
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....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TMP; Similar ligands found: 92
No: Ligand ECFP6 Tc MDL keys Tc
1 TMP 1 1
2 TYD 0.80597 0.985714
3 TTP 0.760563 0.985714
4 UFP 0.716418 0.917808
5 TBD 0.708333 0.945205
6 5HU 0.705882 0.957747
7 BRU 0.705882 0.917808
8 5IU 0.695652 0.917808
9 THM 0.693548 0.859155
10 LLT 0.693548 0.859155
11 NYM 0.671429 0.971831
12 FDM 0.671429 0.931507
13 THP 0.661972 0.985507
14 TLO 0.654321 0.931507
15 0DN 0.646154 0.84507
16 ATM 0.64 0.906667
17 BVP 0.64 0.957747
18 DAU 0.635294 0.918919
19 18T 0.623529 0.918919
20 1JB 0.623529 0.918919
21 TRH 0.623529 0.918919
22 3R2 0.623529 0.906667
23 TDX 0.623529 0.931507
24 DWN 0.609195 0.894737
25 T3Q 0.609195 0.894737
26 3YN 0.609195 0.918919
27 T3F 0.609195 0.894737
28 T46 0.602273 0.918919
29 0N2 0.602273 0.883117
30 T3P 0.6 0.957143
31 DT DT DT DT DT 0.597701 0.958333
32 MMF 0.595506 0.894737
33 0FX 0.595506 0.894737
34 AKM 0.593407 0.873418
35 UMP 0.583333 0.956522
36 DU 0.583333 0.956522
37 QDM 0.582418 0.883117
38 DT DT PST 0.577778 0.893333
39 FNF 0.576087 0.906667
40 JHZ 0.576087 0.871795
41 1YF 0.576087 0.906667
42 TXS 0.575342 0.8
43 4TG 0.569892 0.906667
44 T3S 0.56 0.8
45 2DT 0.555556 0.971429
46 ATY 0.548781 0.931507
47 DDN 0.547945 0.956522
48 AZD 0.535714 0.894737
49 FUH 0.53 0.894737
50 QUH 0.53 0.894737
51 T5A 0.524272 0.829268
52 DT DT DT 0.52381 0.890411
53 DT ME6 DT 0.509804 0.881579
54 DCM 0.506494 0.890411
55 DC 0.506494 0.890411
56 AZZ 0.5 0.789474
57 4TA 0.495327 0.817073
58 ABT 0.483516 0.871795
59 QBT 0.480519 0.915493
60 WMJ 0.477778 0.75
61 7SG 0.474138 0.851852
62 TQP 0.474138 0.851852
63 T4K 0.470085 0.841463
64 T5K 0.470085 0.841463
65 DUD 0.469136 0.942857
66 UMC 0.467532 0.901408
67 D3T 0.464286 0.957747
68 TPE 0.463158 0.881579
69 D4M 0.461538 0.927536
70 ID2 0.452055 0.786667
71 UC5 0.451219 0.929577
72 DUT 0.447059 0.942857
73 DUP 0.44186 0.916667
74 DUN 0.440476 0.916667
75 ADS THS THS THS 0.433628 0.776471
76 DT MA7 DT 0.42623 0.807229
77 8OG 0.425287 0.82716
78 BVD 0.423077 0.821918
79 74X 0.42 0.72093
80 74W 0.42 0.72093
81 5FU 0.4125 0.84
82 D4D 0.411765 0.914286
83 PAX 0.408333 0.839506
84 YYY 0.406977 0.878378
85 DA DT DA DA 0.404959 0.82716
86 BTD 0.404762 0.759494
87 DPB 0.404494 0.890411
88 DUT MG 0.404494 0.876712
89 5BU 0.402439 0.84
90 3DT 0.4 0.821918
91 DUS 0.4 0.820513
92 UMP AF3 PO4 0.4 0.842105
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3B6O; Ligand: TMP; Similar sites found: 36
This union binding pocket(no: 1) in the query (biounit: 3b6o.bio2) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1NHZ 486 0.02017 0.41032 1.61943
2 5V4R MGT 0.01071 0.4046 1.85185
3 3QWI CUE 0.01981 0.43258 2.22222
4 2GOU FMN 0.02572 0.41765 2.42915
5 1USR SIA WIA 0.0031 0.41024 2.83401
6 4A3U FMN 0.02278 0.40599 2.83401
7 5V3Y 5V8 0.01278 0.40497 2.83401
8 1USR SIA 0.004256 0.40427 2.83401
9 3TN7 NJP 0.04527 0.40212 2.83401
10 4HXY NDP 0.03706 0.40684 3.23887
11 4OKE AMP 0.00003625 0.46159 3.64372
12 5E58 CPZ 0.01349 0.40217 3.64372
13 2HBL AMP 0.0003914 0.4947 4.04858
14 2DBZ NAP 0.0436 0.40072 4.04858
15 3MPI GRA 0.02222 0.4376 4.45344
16 5NE5 KIF 0.008859 0.42166 4.45344
17 5DN9 NAD 0.03504 0.41035 4.8583
18 3B2Q ATP 0.02668 0.40549 4.8583
19 3GBR PRP 0.04669 0.40248 4.8583
20 3MJE NDP 0.03368 0.40676 5.26316
21 5ECP MET 0.04101 0.41329 5.38117
22 5ECP JAA 0.04101 0.41329 5.38117
23 5F5N NAD 0.03208 0.40539 5.66802
24 3AMN CBI 0.02624 0.4087 6.07287
25 3AMN CBK 0.02624 0.4087 6.07287
26 1E6E FAD 0.03789 0.41152 6.47773
27 1WLJ U5P 0.0002075 0.44579 6.87831
28 5CSD ACD 0.04372 0.40712 6.91824
29 4NG2 OHN 0.009193 0.43118 7.07965
30 2GTE VA 0.03149 0.40171 7.25806
31 4R74 F6P 0.01688 0.40743 7.69231
32 1W0H AMP 0.000001455 0.59911 8.82353
33 2UUU PL3 0.04606 0.42149 12.1457
34 1FIQ FAD 0.01283 0.43509 12.7854
35 2IDO TMP 0.000000006051 0.65587 29.0323
36 1J54 TMP 0.00000008002 0.56124 29.0323
Pocket No.: 2; Query (leader) PDB : 3B6O; Ligand: TMP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3b6o.bio2) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3B6O; Ligand: TMP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3b6o.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3B6O; Ligand: TMP; Similar sites found: 17
This union binding pocket(no: 4) in the query (biounit: 3b6o.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1DL5 SAH 0.03269 0.40495 2.02429
2 4I8P NAD 0.03595 0.40973 2.83401
3 3RI1 3RH 0.03682 0.40346 2.83401
4 4ZVI 4S4 0.02529 0.40028 2.83401
5 2BL9 CP6 0.02902 0.41788 3.36134
6 2BL9 NDP 0.02902 0.41788 3.36134
7 5EYK 5U5 0.04026 0.40013 3.38983
8 3FC4 EDO 0.01813 0.4426 3.64372
9 4MCC 21X 0.02375 0.41098 4.87805
10 1GOY 3GP 0.007741 0.40175 5.17241
11 1KQ4 FAD 0.01351 0.41936 5.26316
12 5VC5 96M 0.03664 0.40231 6.07287
13 3SUC ATP 0.008259 0.40056 6.88259
14 3ZQ6 ADP ALF 0.03955 0.40054 6.88259
15 1V47 ADX 0.01821 0.40936 10.1215
16 3HRD FAD 0.0239 0.42719 11.7409
17 2UUU FAD 0.02901 0.42888 12.1457
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