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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 SP AND REVEALS A POLYPROLINE II HELIX FOR PROTEIN PARTENRING MUS MUSCULUS PROLINE HELIX NUCLEOTIDE COMPLEX DNAQ FAMILY HYDROLASE
Ref.: THE CRYSTAL STRUCTURE OF TREX1 EXPLAINS THE 3' NUCL SPECIFICITY AND REVEALS A POLYPROLINE II HELIX FOR 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 5 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 4 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 (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
Ligand no: 1; Ligand: D5M; Similar ligands found: 142
No: Ligand ECFP6 Tc MDL keys Tc
1 DA 1 1
2 D5M 1 1
3 DAT 0.816901 0.971831
4 AS 0.808824 0.945205
5 DTP 0.773333 0.971831
6 3L1 0.707692 0.833333
7 3D1 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 6OG 0.580247 0.932432
14 103 0.578947 0.849315
15 AMP 0.558442 0.902778
16 A 0.558442 0.902778
17 A3P 0.54321 0.902778
18 DDS 0.528736 0.916667
19 A2P 0.52439 0.915493
20 DG 0.511905 0.894737
21 DGP 0.511905 0.894737
22 HF7 0.511111 0.958333
23 ZDA 0.505747 0.826667
24 ABM 0.5 0.853333
25 3AT 0.494382 0.90411
26 7D3 0.493976 0.866667
27 DA DT DA DA 0.491379 0.82716
28 ADP 0.482353 0.878378
29 A2D 0.481928 0.853333
30 V3L 0.477778 0.878378
31 DI 0.476744 0.893333
32 2AM 0.475 0.902778
33 PPS 0.472527 0.792683
34 PAP 0.47191 0.890411
35 7D4 0.471264 0.866667
36 ADX 0.471264 0.771084
37 BA3 0.470588 0.853333
38 A12 0.470588 0.893333
39 AP2 0.470588 0.893333
40 3AM 0.469136 0.888889
41 MDR 0.467532 0.780822
42 HEJ 0.465909 0.878378
43 ATP 0.465909 0.878378
44 AP5 0.465116 0.853333
45 B4P 0.465116 0.853333
46 PRX 0.460674 0.855263
47 APC 0.460674 0.893333
48 5FA 0.460674 0.878378
49 2A5 0.460674 0.905405
50 AQP 0.460674 0.878378
51 3AD 0.460526 0.791667
52 AN2 0.45977 0.866667
53 AT4 0.45977 0.844156
54 SRA 0.457831 0.855263
55 OVE 0.457831 0.866667
56 ATR 0.455556 0.902778
57 M33 0.454545 0.842105
58 AU1 0.454545 0.855263
59 CA0 0.454545 0.831169
60 2FD 0.45 0.802632
61 ACP 0.449438 0.88
62 50T 0.449438 0.866667
63 25A 0.447917 0.878378
64 7D7 0.445946 0.753425
65 ACQ 0.445652 0.88
66 T99 0.445652 0.844156
67 TAT 0.445652 0.844156
68 AR6 0.444444 0.853333
69 APR 0.444444 0.853333
70 A1R 0.443299 0.894737
71 A3R 0.443299 0.894737
72 RAB 0.44 0.756757
73 XYA 0.44 0.756757
74 ADN 0.44 0.756757
75 AGS 0.43956 0.833333
76 RBY 0.43956 0.868421
77 SAP 0.43956 0.833333
78 AD9 0.43956 0.855263
79 ADV 0.43956 0.868421
80 CL9 0.4375 0.802632
81 AV2 0.43617 0.853333
82 NA7 0.434343 0.918919
83 6YZ 0.431579 0.88
84 ANP 0.430108 0.855263
85 ADS THS THS THS 0.42735 0.767442
86 A2R 0.427083 0.866667
87 SON 0.426966 0.893333
88 5AL 0.425532 0.842105
89 ANZ 0.424528 0.7875
90 ADP PO3 0.423913 0.851351
91 GGZ 0.42268 0.768293
92 A22 0.42268 0.866667
93 3DH 0.421687 0.714286
94 TM1 0.421569 0.741176
95 DG DA DC DG 0.421053 0.819277
96 ALF ADP 0.421053 0.7875
97 ATF 0.421053 0.844156
98 ADP ALF 0.421053 0.7875
99 A A A 0.42 0.891892
100 5SV 0.418367 0.835443
101 ARJ 0.417722 0.712329
102 SRP 0.416667 0.868421
103 GAP 0.414894 0.807692
104 DGI 0.414894 0.883117
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 LMS 0.411765 0.75
110 PTJ 0.411765 0.8125
111 QQY 0.411765 0.802632
112 FYA 0.411765 0.917808
113 NB8 0.411765 0.835443
114 ACK 0.411765 0.847222
115 5N5 0.410256 0.733333
116 DLL 0.41 0.842105
117 MAP 0.408163 0.833333
118 CC5 0.407895 0.777778
119 3UK 0.405941 0.831169
120 DA DC DG DA 0.405797 0.851852
121 A4D 0.405063 0.733333
122 5CD 0.405063 0.743243
123 8QN 0.40404 0.842105
124 9ZD 0.40404 0.822785
125 OOB 0.40404 0.842105
126 9ZA 0.40404 0.822785
127 9SN 0.403846 0.790123
128 DTA 0.402439 0.75
129 A3G 0.402299 0.763158
130 NEC 0.402299 0.688312
131 2VA 0.402174 0.717949
132 5X8 0.402174 0.75
133 ADP VO4 0.402062 0.842105
134 VO4 ADP 0.402062 0.842105
135 B5V 0.401961 0.820513
136 WAQ 0.401961 0.87013
137 PR8 0.401961 0.860759
138 QQX 0.4 0.792208
139 PAJ 0.4 0.780488
140 AFX 0.4 0.625
141 5AS 0.4 0.727273
142 AMO 0.4 0.868421
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3B6O; Ligand: TMP; Similar sites found with APoc: 101
This union binding pocket(no: 1) in the query (biounit: 3b6o.bio2) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 4YDX TCE None
2 1L6O SER LEU LYS LEU MET THR THR VAL None
3 5Z2L NDP None
4 3TD3 GLY None
5 1XSE NDP 0.809717
6 5WHU SIA GAL 1.21457
7 1UHK CZN 1.57068
8 5FMD NYT 1.61943
9 1NHZ 486 1.61943
10 5V4R MGT 1.85185
11 3C8Z 5CA 2.02429
12 4ITH RCM 2.02429
13 3QWI CUE 2.22222
14 2GOU FMN 2.42915
15 1RJW ETF 2.42915
16 5BVE 4VG 2.42915
17 2BNJ XYP XYP AHR FER 2.42915
18 1SR7 MOF 2.42915
19 4YSW FAD 2.83401
20 4YSW NAI 2.83401
21 1X7D ORN 2.83401
22 5HXI FAD 2.83401
23 5FPE 3TR 2.83401
24 1USR SIA WIA 2.83401
25 3GMB FAD 2.83401
26 1J49 NAD 2.83401
27 4A3U FMN 2.83401
28 5V3Y 5V8 2.83401
29 1USR SIA 2.83401
30 4C2V YJA 2.83401
31 5CX6 CDP 2.83401
32 3TN7 NJP 2.83401
33 5FPN KYD 2.83401
34 5AZC PGT 3.23887
35 4BXK 1IU 3.23887
36 4CA5 3EF 3.23887
37 4HXY NDP 3.23887
38 4D7E FAD 3.23887
39 4Q9M FPP 3.23887
40 4OKE AMP 3.64372
41 1KRP DT DT PST 3.64372
42 4XT8 NAP 3.64372
43 4XT8 TMQ 3.64372
44 3RFV 15L 3.64372
45 5W8Q BU4 3.64372
46 5E58 CPZ 3.64372
47 4G6I RS3 3.80952
48 2HBL AMP 4.04858
49 4LHD GLY 4.04858
50 2DBZ NAP 4.04858
51 1O94 ADP 4.04858
52 6D6L FY4 4.11765
53 1RM6 FAD 4.34783
54 3MPI GRA 4.45344
55 5NE5 KIF 4.45344
56 3A28 NAD 4.45344
57 6ACS CIT 4.45344
58 1PVC ILE SER GLU VAL 4.62185
59 2VAP GDP 4.67033
60 2RH4 EMO 4.8583
61 2NAD NAD 4.8583
62 5DN9 NAD 4.8583
63 3B2Q ATP 4.8583
64 1KQ4 FAD 5.26316
65 3IHG FAD 5.26316
66 2AF6 FAD 5.26316
67 2GQ2 NAP 5.26316
68 3O5N BR0 5.35714
69 5ECP MET 5.38117
70 5ECP JAA 5.38117
71 4QVB F42 5.44218
72 5F5N NAD 5.66802
73 1T3Q MCN 5.66802
74 1NBU PH2 5.88235
75 1FO3 KIF 6.07287
76 3AMN CBK 6.07287
77 3AMN CBI 6.07287
78 3LL5 IPE 6.07287
79 3LL5 ADP 6.07287
80 1E6E FAD 6.47773
81 1WLJ U5P 6.87831
82 5CSD ACD 6.91824
83 4NG2 OHN 7.07965
84 2GTE VA 7.25806
85 4R74 F6P 7.69231
86 6H3O FAD 8.09717
87 1W0H AMP 8.82353
88 5AE2 FYC 9.31174
89 5AE2 FAD 9.31174
90 1Q0H NDP 9.7166
91 4EN4 GT0 10.1215
92 3GPO APR 11.3095
93 1V97 FAD 11.336
94 2UUU FAD 12.1457
95 2UUU PL3 12.1457
96 1FIQ FAD 12.7854
97 1U7Z PMT 14.1593
98 5W7B MYR 14.1844
99 3NRZ FAD 17.0732
100 2IDO TMP 29.0323
101 1J54 TMP 29.0323
Pocket No.: 2; Query (leader) PDB : 3B6O; Ligand: TMP; Similar sites found with APoc: 54
This union binding pocket(no: 2) in the query (biounit: 3b6o.bio2) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 1NU4 MLA None
2 3GQK ATP None
3 2J7T 274 1.61943
4 1J0D 5PA 1.61943
5 4P5E N6P 1.97368
6 2HY0 306 2.02429
7 6AYR BIG 2.02429
8 2HJR APR 2.13415
9 2CWH PYC 2.42915
10 2CWH NDP 2.42915
11 6F5W KG1 2.42915
12 3UBM COA 2.42915
13 5EH0 5NW 2.42915
14 3E5A VX6 2.83401
15 1AE1 NAP 2.83401
16 3RI1 3RH 2.83401
17 4LZJ 22H 2.83401
18 5MDH NAD 2.83401
19 6CEP NAD 3.23887
20 2GRU NAD 3.23887
21 4R57 ACO 3.40909
22 5J62 FMN 3.4632
23 3FC4 EDO 3.64372
24 5JGA 6KC 3.64372
25 3A06 NDP 3.7234
26 1DKU AP2 4.04858
27 2AHR NAP 4.04858
28 2H8H H8H 4.04858
29 4G5H UD7 4.45344
30 4E70 N7I 4.45344
31 5OVK NDP 4.45344
32 5JKG 6LF 4.8583
33 5EXE 5SR 4.8583
34 3PP0 03Q 4.8583
35 2J4K U5P 4.86726
36 4M52 FAD 5.26316
37 3LXK MI1 5.26316
38 3IGZ 3PG 5.66802
39 3IGZ 2PG 5.66802
40 5OCA 9QZ 5.66802
41 5VC5 96M 6.07287
42 1FFU CDP 6.13497
43 2X2M X2M 6.36943
44 1JG3 ADN 6.47773
45 3SUC ATP 6.88259
46 3ZQ6 ADP ALF 6.88259
47 1TOI HCI 6.88259
48 5T79 NDP 8.09717
49 6F8B CXH 8.50202
50 1JPA ANP 9.29487
51 2Z49 AMG 9.31174
52 2Z48 NGA 9.31174
53 1NFQ NAI 10.5263
54 6GIN IR2 10.9312
Pocket No.: 3; Query (leader) PDB : 3B6O; Ligand: TMP; Similar sites found with APoc: 15
This union binding pocket(no: 3) in the query (biounit: 3b6o.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 1QV1 CZH 1.53846
2 4RF2 NAP 2.20588
3 5LGA 6VH 2.42915
4 4H6Q TFB 2.42915
5 1ICP FMN 2.42915
6 1X7D NAD 2.83401
7 1PVN MZP 3.64372
8 5B47 PYR 3.64372
9 5NDF UDP 3.64372
10 5NDF LU2 3.64372
11 1Q7E MET 4.04858
12 3ABA FLI 5.26316
13 4OSP NAP 6.07287
14 1JF0 CZH 8.20513
15 1Q0H FOM 9.7166
Pocket No.: 4; Query (leader) PDB : 3B6O; Ligand: TMP; Similar sites found with APoc: 27
This union binding pocket(no: 4) in the query (biounit: 3b6o.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 1US5 GLU 1.21457
2 3RG9 NDP 1.66667
3 1DL5 SAH 2.02429
4 1OPK P16 2.42915
5 4CDN FAD 2.42915
6 4I8P NAD 2.83401
7 4ZVI 4S4 2.83401
8 3ZKK XYP XYP XYP XYP 3.23887
9 2BL9 CP6 3.36134
10 2BL9 NDP 3.36134
11 5EYK 5U5 3.38983
12 1QMG APX 3.64372
13 4XYB NDP 4.04858
14 1F0X FAD 4.04858
15 1ZDU P3A 4.8583
16 4MCC 21X 4.87805
17 1WN3 HXC 5.88235
18 2VZ0 D64 6.47773
19 2VZ0 NAP 6.47773
20 5Y6Q FAD 6.79012
21 4ZOH FAD 7.28745
22 5J60 FAD 8.09717
23 2RDG NDG FUC SIA GAL 8.67347
24 1V47 ADX 10.1215
25 3HRD FAD 11.7409
26 1N62 FAD 14.4578
27 5Z84 CHD 25
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