Receptor
PDB id Resolution Class Description Source Keywords
2JAO 2 Å EC: 3.1.3.- CRYSTAL STRUCTURE OF D12N VARIANT OF MOUSE CYTOSOLIC 5'(3')- DEOXYRIBONUCLEOTIDASE (CDN) IN COMPLEX WITH DEOXYGUANOSINE M ONOPHOSPHATE MUS MUSCULUS NUCLEOTIDE METABOLISM NUCLEOTIDE-BINDING ALPHA-BETA FOLD BINDING HYDROLASE MAGNESIUM CYTOSOL
Ref.: CRYSTAL STRUCTURES OF HUMAN AND MURINE DEOXYRIBONUCLEOTIDASES: INSIGHTS INTO RECOGNITION O SUBSTRATES AND NUCLEOTIDE ANALOGUES. BIOCHEMISTRY V. 46 13809 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DGP A:1201;
Valid;
none;
submit data
347.221 C10 H14 N5 O7 P c1nc2...
GOL A:1200;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
MG A:1202;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2JAR 1.94 Å EC: 3.1.3.- CRYSTAL STRUCTURE OF D12N VARIANT OF MOUSE CYTOSOLIC 5'(3')- DEOXYRIBONUCLEOTIDASE (CDN) IN COMPLEX WITH DEOXYURIDINE 5'M ONOPHOSPHATE MUS MUSCULUS NUCLEOTIDE METABOLISM NUCLEOTIDE-BINDING ALFA BETA FOLD MBINDING TRANSIT PEPTIDE HYDROLASE CYTOSOLIC MAGNESIUM BINDING
Ref.: CRYSTAL STRUCTURES OF HUMAN AND MURINE DEOXYRIBONUCLEOTIDASES: INSIGHTS INTO RECOGNITION O SUBSTRATES AND NUCLEOTIDE ANALOGUES. BIOCHEMISTRY V. 46 13809 2007
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 2JAR - UMP C9 H13 N2 O8 P C1[C@@H]([....
2 2JAO - DGP C10 H14 N5 O7 P c1nc2c(n1[....
70% Homology Family (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 1Q92 - DRM C10 H15 N2 O6 P C1C[C@H]([....
2 1Z4P - DGP C10 H14 N5 O7 P c1nc2c(n1[....
3 1Z4M - U5P C9 H13 N2 O9 P C1=CN(C(=O....
4 4NFL Ki = 22.1 uM 2JW C17 H18 N3 O10 P CC1=CN(C(=....
5 1Q91 Ki = 70 uM DPB C17 H19 N2 O8 P CC1=CN(C(=....
6 2JAU - ATM C10 H14 N5 O7 P CC1=CN(C(=....
7 1Z4K - T3P C10 H15 N2 O8 P CC1=CN(C(=....
8 2JAW - BVP C11 H14 Br N2 O8 P C1[C@@H]([....
9 1Z4L - TMP C10 H15 N2 O8 P CC1=CN(C(=....
10 4L6C Ki = 2.71 uM 0BT C17 H18 I N2 O8 P CC1=CN(C(=....
11 1Z4Q - D4M C10 H13 N2 O7 P CC1=CN(C(=....
12 4MWO Ki = 7.9 uM 2E2 C18 H19 N2 O10 P CC1=CN(C(=....
13 1Z4I - UMP C9 H13 N2 O8 P C1[C@@H]([....
14 1Z4J - U2P C9 H13 N2 O9 P C1=CN(C(=O....
15 2JAR - UMP C9 H13 N2 O8 P C1[C@@H]([....
16 2JAO - DGP C10 H14 N5 O7 P c1nc2c(n1[....
50% Homology Family (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 1Q92 - DRM C10 H15 N2 O6 P C1C[C@H]([....
2 1Z4P - DGP C10 H14 N5 O7 P c1nc2c(n1[....
3 1Z4M - U5P C9 H13 N2 O9 P C1=CN(C(=O....
4 4NFL Ki = 22.1 uM 2JW C17 H18 N3 O10 P CC1=CN(C(=....
5 1Q91 Ki = 70 uM DPB C17 H19 N2 O8 P CC1=CN(C(=....
6 2JAU - ATM C10 H14 N5 O7 P CC1=CN(C(=....
7 1Z4K - T3P C10 H15 N2 O8 P CC1=CN(C(=....
8 2JAW - BVP C11 H14 Br N2 O8 P C1[C@@H]([....
9 1Z4L - TMP C10 H15 N2 O8 P CC1=CN(C(=....
10 4L6C Ki = 2.71 uM 0BT C17 H18 I N2 O8 P CC1=CN(C(=....
11 1Z4Q - D4M C10 H13 N2 O7 P CC1=CN(C(=....
12 4MWO Ki = 7.9 uM 2E2 C18 H19 N2 O10 P CC1=CN(C(=....
13 1Z4I - UMP C9 H13 N2 O8 P C1[C@@H]([....
14 1Z4J - U2P C9 H13 N2 O9 P C1=CN(C(=O....
15 2JAR - UMP C9 H13 N2 O8 P C1[C@@H]([....
16 2JAO - DGP C10 H14 N5 O7 P c1nc2c(n1[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: DGP; Similar ligands found: 78
No: Ligand ECFP6 Tc MDL keys Tc
1 DGP 1 1
2 DG 1 1
3 DGI 0.815789 0.986842
4 DGT 0.775 0.986842
5 DI 0.62963 0.973333
6 5GP 0.60241 0.922078
7 G 0.60241 0.922078
8 CGP 0.596154 0.925926
9 GDP 0.516484 0.910256
10 GH3 0.515789 0.935065
11 DA 0.511905 0.894737
12 D5M 0.511905 0.894737
13 3GP 0.505747 0.909091
14 2GP 0.505747 0.922078
15 GP3 0.505495 0.8875
16 G3D 0.505263 0.922078
17 GTP 0.5 0.910256
18 GP2 0.5 0.924051
19 G4P 0.494845 0.922078
20 GNH 0.494624 0.898734
21 P2G 0.494382 0.871795
22 G2P 0.489583 0.924051
23 GMP 0.487805 0.797468
24 GMV 0.484211 0.8875
25 ALF 5GP 0.484211 0.833333
26 P1G 0.483516 0.884615
27 G2R 0.48 0.948718
28 GAV 0.479592 0.876543
29 GCP 0.479167 0.911392
30 G1R 0.479167 0.898734
31 6OG 0.477778 0.886076
32 0O2 0.475248 0.922078
33 GSP 0.474227 0.865854
34 9GM 0.474227 0.8875
35 GNP 0.474227 0.8875
36 3PD UM3 0.473214 0.878049
37 DOI 0.47191 0.87013
38 6MA 0.47191 0.858974
39 GDP BEF 0.463918 0.875
40 GPG 0.460784 0.876543
41 GPX 0.46 0.909091
42 GTP MG 0.459184 0.897436
43 GDP ALF 0.455446 0.833333
44 3ZE 0.451613 0.897436
45 CF2 0.451613 0.811765
46 GPD 0.449541 0.890244
47 GDC 0.443396 0.876543
48 GKE 0.443396 0.876543
49 Y9Z 0.443396 0.869048
50 GDD 0.443396 0.876543
51 GDP AF3 0.441176 0.833333
52 G3A 0.435185 0.8875
53 YGP 0.433962 0.845238
54 KB7 0.43299 0.795181
55 G5P 0.431193 0.8875
56 SGP 0.430108 0.817073
57 JB2 0.427273 0.876543
58 GTG 0.425926 0.855422
59 GFB 0.425926 0.876543
60 GDR 0.425926 0.876543
61 DAT 0.425532 0.896104
62 6CK 0.422018 0.855422
63 DZ4 0.418367 0.873418
64 GKD 0.414414 0.876543
65 DU DU DU DU BRU DG DU 0.414062 0.827586
66 BGO 0.413793 0.865854
67 U2G 0.413793 0.855422
68 GDX 0.410714 0.8875
69 DTP 0.408163 0.896104
70 CG2 0.40678 0.855422
71 AS 0.406593 0.85
72 KBD 0.40566 0.795181
73 GDP 7MG 0.405405 0.853659
74 JB3 0.405172 0.865854
75 UCG 0.404762 0.876543
76 8OG 0.404255 0.855422
77 FEG 0.401709 0.869048
78 NGD 0.401709 0.876543
Similar Ligands (3D)
Ligand no: 1; Ligand: DGP; Similar ligands found: 138
No: Ligand Similarity coefficient
1 AMP 0.9601
2 EO7 0.9578
3 IMP 0.9534
4 IMU 0.9501
5 XMP 0.9482
6 71V 0.9463
7 LMS 0.9455
8 45A 0.9444
9 BRU 0.9429
10 AMP MG 0.9427
11 G7M 0.9411
12 TMP 0.9400
13 5CM 0.9389
14 SRA 0.9387
15 93A 0.9368
16 8BR 0.9361
17 IRP 0.9348
18 6CG 0.9338
19 UFP 0.9327
20 ABM 0.9326
21 FMP 0.9325
22 6MZ 0.9292
23 JLN 0.9248
24 N5O 0.9227
25 7D5 0.9225
26 ZAS 0.9220
27 8GM 0.9218
28 5IU 0.9217
29 8OP 0.9208
30 5HU 0.9198
31 PCG 0.9192
32 NEC 0.9165
33 CMP 0.9164
34 UMP 0.9149
35 U5P 0.9142
36 QBT 0.9139
37 A3N 0.9120
38 3DH 0.9120
39 AOC 0.9116
40 5FU 0.9112
41 CNU 0.9109
42 Z8B 0.9109
43 5BU 0.9107
44 J7C 0.9085
45 6RE 0.9085
46 9L3 0.9062
47 MTA 0.9057
48 5AS 0.9037
49 NYM 0.9036
50 DCM 0.9027
51 4X2 0.9012
52 C2R 0.9000
53 EP4 0.8996
54 C 0.8994
55 NMN 0.8993
56 5HM 0.8985
57 35G 0.8960
58 NWQ 0.8960
59 U 0.8958
60 2DT 0.8950
61 DU 0.8948
62 AMZ 0.8940
63 TKW 0.8940
64 T3S 0.8938
65 NCN 0.8934
66 DUS 0.8931
67 75G 0.8930
68 6SW 0.8928
69 FDM 0.8927
70 PFU 0.8920
71 RVP 0.8918
72 MCF 0.8907
73 C5P 0.8904
74 SSI 0.8902
75 D4M 0.8896
76 CA0 0.8892
77 H2U 0.8881
78 UP6 0.8877
79 SP1 0.8876
80 NIA 0.8876
81 CAR 0.8876
82 TXS 0.8875
83 BVP 0.8875
84 RP1 0.8868
85 FNU 0.8863
86 PSU 0.8839
87 O8M 0.8833
88 GNG 0.8826
89 7CH 0.8825
90 ACJ 0.8811
91 T7O 0.8808
92 UMC 0.8804
93 3Q1 0.8800
94 16B 0.8791
95 0NU 0.8781
96 TZY 0.8775
97 581 0.8765
98 43H 0.8762
99 ATM 0.8761
100 6SZ 0.8758
101 ADP 0.8750
102 6J7 0.8746
103 2FA 0.8744
104 4UO 0.8742
105 CL9 0.8735
106 KG4 0.8733
107 3D1 0.8728
108 0JB 0.8727
109 PWH 0.8722
110 DC 0.8718
111 JP3 0.8709
112 8HG 0.8694
113 SNP 0.8693
114 M8Q 0.8690
115 103 0.8687
116 PRX 0.8686
117 ADN 0.8682
118 M7G 0.8681
119 DSH 0.8675
120 100 0.8675
121 3L6 0.8671
122 3F5 0.8670
123 IXF 0.8664
124 FMC 0.8634
125 460 0.8627
126 HDU 0.8623
127 PY1 0.8619
128 IYX 0.8606
129 JFX 0.8595
130 NOS 0.8594
131 XTK 0.8584
132 A 0.8575
133 5N5 0.8575
134 FN5 0.8574
135 9ST 0.8566
136 A4D 0.8535
137 RFZ 0.8526
138 QTJ 0.8518
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2JAR; Ligand: UMP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2jar.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2JAR; Ligand: UMP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2jar.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
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