-->
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'- MONOPHOSPHATE MUS MUSCULUS NUCLEOTIDE METABOLISM NUCLEOTIDE-BINDING NUCLEOTIDE- BINDING ALFA BETA FOLD METAL- BINDING TRANSIT PEPTIDE HYDROLASE CYTOSOLIC MAGNESIUM METAL-BINDING
Ref.: CRYSTAL STRUCTURES OF HUMAN AND MURINE DEOXYRIBONUCLEOTIDASES: INSIGHTS INTO RECOGNITION OF 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 7 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
Ligand no: 1; Ligand: DGP; Similar ligands found: 85
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 DG DG 0.693182 0.925
6 DI 0.62963 0.973333
7 5GP 0.60241 0.922078
8 G 0.60241 0.922078
9 CGP 0.596154 0.925926
10 DC DG 0.575472 0.902439
11 GDP 0.516484 0.910256
12 GH3 0.515789 0.935065
13 DA 0.511905 0.894737
14 D5M 0.511905 0.894737
15 3GP 0.505747 0.909091
16 2GP 0.505747 0.922078
17 GP3 0.505495 0.8875
18 G3D 0.505263 0.922078
19 GTP 0.5 0.910256
20 GP2 0.5 0.924051
21 G4P 0.494845 0.922078
22 GNH 0.494624 0.898734
23 P2G 0.494382 0.871795
24 G2P 0.489583 0.924051
25 GMP 0.487805 0.797468
26 ALF 5GP 0.484211 0.833333
27 GMV 0.484211 0.8875
28 P1G 0.483516 0.884615
29 G2R 0.48 0.948718
30 GAV 0.479592 0.876543
31 GCP 0.479167 0.911392
32 G1R 0.479167 0.898734
33 6OG 0.477778 0.886076
34 0O2 0.475248 0.922078
35 GNP 0.474227 0.8875
36 9GM 0.474227 0.8875
37 GSP 0.474227 0.865854
38 3PD UM3 0.473214 0.878049
39 DOI 0.47191 0.87013
40 DG DA DC DG 0.469697 0.891566
41 DG DC 0.466667 0.9375
42 GPG 0.460784 0.876543
43 GPX 0.46 0.909091
44 GDP ALF 0.455446 0.833333
45 ALF GDP 0.455446 0.833333
46 CF2 0.451613 0.811765
47 3ZE 0.451613 0.897436
48 DA DU DG DA 0.451327 0.845238
49 GPD 0.449541 0.890244
50 GDC 0.443396 0.876543
51 Y9Z 0.443396 0.869048
52 GKE 0.443396 0.876543
53 GDD 0.443396 0.876543
54 GCP G 0.442308 0.884615
55 DA DC DG DA 0.442029 0.925926
56 GDP AF3 0.441176 0.833333
57 G3A 0.435185 0.8875
58 YGP 0.433962 0.845238
59 DC DG DA DC 0.431818 0.91358
60 G5P 0.431193 0.8875
61 SGP 0.430108 0.817073
62 JB2 0.427273 0.876543
63 GDR 0.425926 0.876543
64 G G 0.425926 0.8875
65 GFB 0.425926 0.876543
66 GTG 0.425926 0.855422
67 DAT 0.425532 0.896104
68 6CK 0.422018 0.855422
69 DT DA DC DG 0.42069 0.870588
70 DC DG DT DA 0.417808 0.870588
71 GKD 0.414414 0.876543
72 DU DU DU DU BRU DG DU 0.414062 0.827586
73 BGO 0.413793 0.865854
74 U2G 0.413793 0.855422
75 GDX 0.410714 0.8875
76 DTP 0.408163 0.896104
77 CG2 0.40678 0.855422
78 AS 0.406593 0.85
79 GDP 7MG 0.405405 0.853659
80 JB3 0.405172 0.865854
81 UCG 0.404762 0.876543
82 8OG 0.404255 0.855422
83 FEG 0.401709 0.869048
84 NGD 0.401709 0.876543
85 G A A A 0.4 0.864198
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: 56
This union binding pocket(no: 1) in the query (biounit: 2jar.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 5HDA SER MET PRO GLU LEU SER PRO VAL LEU None
2 4OWK NGA None
3 1YNS HPO 1
4 2HIM ASN 2
5 2HIM ASP 2
6 5UI2 SUC 2
7 1HV6 MAW MAV GCU 2
8 5WHU SIA GAL 2.01342
9 4ZEV M6P 2.5
10 1RQL VSO 2.5
11 5DX9 T6P 3
12 1RJW ETF 3
13 3THR C2F 3.5
14 2NZ5 226 3.5
15 1Z5U CMP 3.5
16 1RM0 D6P 3.5
17 3NV3 GAL NAG MAN 3.62319
18 3UXH UXH 4
19 3UXH FAD 4
20 6B2W AG2 4
21 2DC1 CIT 4
22 1L7N ALF 4.5
23 1L7N AF3 4.5
24 1L7P SEP 4.5
25 2RBK VN4 4.5
26 5CGM MAL 4.5
27 4UME KDO 4.66321
28 1QH9 LAC 5
29 2HBL AMP 5
30 4PPF FLC 5
31 1JPA ANP 5
32 6BR7 BEF 5.26316
33 4IF4 BEF 6
34 2YN4 39J 6
35 1L5Y BEF 6.45161
36 6EOM ALA LYS 6.5
37 2FPU HSO 6.81818
38 4G9N NGA 6.99301
39 3A1C ACP 7
40 1G0H IPD 7
41 2P69 PLP 7.5
42 3FGZ BEF 7.8125
43 5O0B 9FE 8.02469
44 5AHO TLA 9
45 3EF0 ALF 9.5
46 1Z4O GL1 9.5
47 1RY2 AMP 9.5
48 3ALT MLB 9.55414
49 1TE2 PGA 10.5
50 4FE3 U5P 12
51 1P6O HPY 12.4224
52 3OCZ SRA 12.5
53 4K30 NLG 13.125
54 2FKA BEF 13.9535
55 3FXU TSU 14.5
56 5W3X ACO 18.75
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
APoc FAQ
Feedback