Receptor
PDB id Resolution Class Description Source Keywords
2IOC 2.1 Å EC: 3.1.11.2 THE CRYSTAL STRUCTURE OF TREX1 EXPLAINS THE 3' NUCLEOTIDE SPECIFICITY AND REVEALS A POLYPROLINE II HELIX FOR PROTEIN P ARTENRING MUS MUSCULUS PROLINE HELIX NUCLEOTIDE COMPLEX DNAQ FAMILY HYDROLASE
Ref.: THE CRYSTAL STRUCTURE OF TREX1 EXPLAINS THE 3' NUCLEOTIDE SPECIFICITY AND REVEALS A POLYPROLINE II HELIX FOR PROTEIN PARTNERING. J.BIOL.CHEM. V. 282 10537 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
D5M A:302;
B:303;
Valid;
Valid;
none;
none;
submit data
331.222 C10 H14 N5 O6 P c1nc(...
MN A:403;
A:404;
B:401;
B:402;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
54.938 Mn [Mn+2...
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: D5M; Similar ligands found: 137
No: Ligand ECFP6 Tc MDL keys Tc
1 D5M 1 1
2 DA 1 1
3 DAT 0.816901 0.971831
4 AS 0.808824 0.945205
5 DTP 0.773333 0.971831
6 3D1 0.707692 0.833333
7 3L1 0.707692 0.833333
8 DOI 0.68 0.916667
9 5F1 0.661765 0.816901
10 101 0.613333 0.943662
11 CPA 0.585859 0.860759
12 7D5 0.581081 0.890411
13 103 0.578947 0.849315
14 AMP 0.558442 0.902778
15 A 0.558442 0.902778
16 A3P 0.54321 0.902778
17 DDS 0.528736 0.916667
18 A2P 0.52439 0.915493
19 DG 0.511905 0.894737
20 DGP 0.511905 0.894737
21 ZDA 0.505747 0.826667
22 ABM 0.5 0.853333
23 3AT 0.494382 0.90411
24 7D3 0.493976 0.866667
25 DA DT DA DA 0.491379 0.82716
26 ADP 0.482353 0.878378
27 A2D 0.481928 0.853333
28 V3L 0.477778 0.878378
29 DI 0.476744 0.893333
30 2AM 0.475 0.902778
31 PPS 0.472527 0.792683
32 PAP 0.47191 0.890411
33 ADX 0.471264 0.771084
34 7D4 0.471264 0.866667
35 A12 0.470588 0.893333
36 BA3 0.470588 0.853333
37 AP2 0.470588 0.893333
38 AMP MG 0.46988 0.828947
39 3AM 0.469136 0.888889
40 MDR 0.467532 0.780822
41 DU DU DU DU BRU DA DU 0.467213 0.807229
42 ATP 0.465909 0.878378
43 AP5 0.465116 0.853333
44 B4P 0.465116 0.853333
45 PRX 0.460674 0.855263
46 2A5 0.460674 0.905405
47 5FA 0.460674 0.878378
48 APC 0.460674 0.893333
49 AQP 0.460674 0.878378
50 3AD 0.460526 0.791667
51 AN2 0.45977 0.866667
52 SRA 0.457831 0.855263
53 OVE 0.457831 0.866667
54 ATR 0.455556 0.902778
55 AU1 0.454545 0.855263
56 M33 0.454545 0.842105
57 CA0 0.454545 0.831169
58 2FD 0.45 0.802632
59 50T 0.449438 0.866667
60 ACP 0.449438 0.88
61 25A 0.447917 0.878378
62 7D7 0.445946 0.753425
63 ACQ 0.445652 0.88
64 TAT 0.445652 0.844156
65 APR 0.444444 0.853333
66 AR6 0.444444 0.853333
67 A1R 0.443299 0.894737
68 RAB 0.44 0.756757
69 ADN 0.44 0.756757
70 XYA 0.44 0.756757
71 ADV 0.43956 0.868421
72 AD9 0.43956 0.855263
73 RBY 0.43956 0.868421
74 AGS 0.43956 0.833333
75 SAP 0.43956 0.833333
76 ADP MG 0.438202 0.818182
77 CL9 0.4375 0.802632
78 AV2 0.43617 0.853333
79 NA7 0.434343 0.918919
80 ADP BEF 0.433333 0.797468
81 BEF ADP 0.433333 0.797468
82 ANP 0.430108 0.855263
83 DA DC DG DA 0.428571 0.819277
84 A2R 0.427083 0.866667
85 SON 0.426966 0.893333
86 5AL 0.425532 0.842105
87 ANZ 0.424528 0.7875
88 ADP PO3 0.423913 0.851351
89 GGZ 0.42268 0.768293
90 A22 0.42268 0.866667
91 3DH 0.421687 0.714286
92 TM1 0.421569 0.741176
93 ATF 0.421053 0.844156
94 ADP ALF 0.421053 0.7875
95 DG DA DC DG 0.421053 0.819277
96 ALF ADP 0.421053 0.7875
97 A A A 0.42 0.891892
98 ATP MG 0.419355 0.818182
99 5SV 0.418367 0.835443
100 ARJ 0.417722 0.712329
101 SRP 0.416667 0.868421
102 ANP MG 0.416667 0.810127
103 DGI 0.414894 0.883117
104 GAP 0.414894 0.807692
105 MTA 0.414634 0.714286
106 4AD 0.414141 0.857143
107 ADQ 0.414141 0.831169
108 ZZB 0.412281 0.761905
109 ACK 0.411765 0.847222
110 PTJ 0.411765 0.8125
111 NB8 0.411765 0.835443
112 QQY 0.411765 0.802632
113 FYA 0.411765 0.917808
114 5N5 0.410256 0.733333
115 DLL 0.41 0.842105
116 MAP 0.408163 0.833333
117 CC5 0.407895 0.777778
118 3UK 0.405941 0.831169
119 5CD 0.405063 0.743243
120 A4D 0.405063 0.733333
121 OOB 0.40404 0.842105
122 8QN 0.40404 0.842105
123 9SN 0.403846 0.790123
124 DTA 0.402439 0.75
125 NEC 0.402299 0.688312
126 A3G 0.402299 0.763158
127 2VA 0.402174 0.717949
128 5X8 0.402174 0.75
129 VO4 ADP 0.402062 0.842105
130 ADP VO4 0.402062 0.842105
131 WAQ 0.401961 0.87013
132 PR8 0.401961 0.860759
133 QQX 0.4 0.792208
134 5AS 0.4 0.727273
135 AFX 0.4 0.625
136 AMO 0.4 0.868421
137 PAJ 0.4 0.780488
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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