Receptor
PDB id Resolution Class Description Source Keywords
2JAU 1.8 Å EC: 3.1.3.5 CRYSTAL STRUCTURE OF D41N VARIANT OF HUMAN MITOCHONDRIAL 5'( DEOXYRIBONUCLEOTIDASE (MDN) IN COMPLEX WITH 3'-AZIDOTHYMIDIM ONOPHOSPHATE HOMO SAPIENS TRANSIT PEPTIDE NUCLEOTIDE-BINDING MITOCHONDRIAL METAL-BIALFA BETA FOLD NUCLEOTIDE- BINDING NUCLEOTIDE METABOLISMHYDROLASE MAGNESIUM MITOCHONDRION
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
ATM A:1230;
 Valid;
 none;
 submit data
347.221 C10 H14 N5 O7 P CC1=C...
MG A:1228;
A:1231;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
24.305 Mg [Mg+2...
PO4 A:1229;
 Invalid;
 none;
 submit data
94.971 O4 P [O-]P...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4L6C 1.8 Å EC: 3.1.3.5 CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL DEOXYRIBONUCLEOTIDA COMPLEX WITH THE INHIBITOR PIB-T HOMO SAPIENS 5-prime -NUCLEOTIDASE MITOCHONDRIA PROTEIN CONFORMATION SEQUENCHOMOLOGY HAD-LIKE HYDROLASE DEPHOSPHORYLATION PHOSPHORYHYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: CONFORMATIONALLY CONSTRAINED NUCLEOSIDE PHOSPHONIC POTENT INHIBITORS OF HUMAN MITOCHONDRIAL AND CYTOSO 5'(3')-NUCLEOTIDASES. ORG.BIOMOL.CHEM. V. 12 7971 2014
Members (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 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....
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: ATM; Similar ligands found: 52
No: Ligand ECFP6 Tc MDL keys Tc
1 ATM 1 1
2 AZD 0.813333 0.986667
3 ABT 0.753086 0.961039
4 AZZ 0.728571 0.88
5 TMP 0.64 0.906667
6 FDM 0.61039 0.871795
7 NYM 0.61039 0.907895
8 THP 0.602564 0.918919
9 TYD 0.542169 0.894737
10 T3P 0.525641 0.893333
11 2DT 0.525641 0.906667
12 TTP 0.517241 0.894737
13 Z5A 0.517241 0.847059
14 LLT 0.513514 0.779221
15 THM 0.513514 0.779221
16 TBD 0.494253 0.884615
17 ATY 0.488889 0.871795
18 0DN 0.480519 0.766234
19 TTP MG 0.477778 0.893333
20 5HU 0.464286 0.87013
21 DAU 0.46 0.8375
22 TLO 0.453608 0.848101
23 UFP 0.452381 0.835443
24 18T 0.45 0.8375
25 TRH 0.45 0.8375
26 1JB 0.45 0.8375
27 TDX 0.45 0.848101
28 9RC 0.44898 0.855422
29 BRU 0.447059 0.835443
30 0FX 0.446602 0.839506
31 5IU 0.44186 0.835443
32 T3Q 0.441176 0.839506
33 T3F 0.441176 0.839506
34 QDM 0.438095 0.829268
35 T46 0.436893 0.8375
36 3R2 0.435644 0.82716
37 TXS 0.435294 0.75
38 FNF 0.433962 0.85
39 1YF 0.433962 0.85
40 MMF 0.432692 0.839506
41 4TG 0.429907 0.85
42 D3T 0.428571 0.894737
43 DWN 0.427184 0.839506
44 3YN 0.427184 0.8375
45 T3S 0.425287 0.75
46 D4M 0.423529 0.864865
47 0N2 0.423077 0.829268
48 JHZ 0.420561 0.819277
49 AKM 0.420561 0.821429
50 TPE 0.417476 0.82716
51 BVP 0.413043 0.87013
52 3DR DT DT DT DT DT 0.40367 0.858974
Similar Ligands (3D)
Ligand no: 1; Ligand: ATM; Similar ligands found: 52
No: Ligand Similarity coefficient
1 UMP 0.9158
2 DU 0.9120
3 5FU 0.9108
4 TKW 0.9063
5 5BU 0.9055
6 QBT 0.9054
7 DC 0.9043
8 5CM 0.9039
9 DUS 0.9035
10 AMP 0.9025
11 U5P 0.9024
12 UMC 0.8977
13 C5P 0.8973
14 UP6 0.8961
15 D5M 0.8952
16 DA 0.8951
17 DDN 0.8950
18 G 0.8950
19 U 0.8944
20 DCM 0.8938
21 C 0.8938
22 CNU 0.8921
23 QTM 0.8915
24 IMP 0.8906
25 AS 0.8898
26 FNU 0.8896
27 A3P 0.8869
28 6MA 0.8858
29 BMP 0.8840
30 IRP 0.8823
31 NUP 0.8810
32 5GP 0.8807
33 71V 0.8797
34 H2U 0.8794
35 FN5 0.8791
36 9L3 0.8778
37 FMP 0.8775
38 BMQ 0.8774
39 PFU 0.8765
40 DGP 0.8761
41 DG 0.8761
42 8OG 0.8753
43 NCN 0.8727
44 16B 0.8723
45 XMP 0.8716
46 IMU 0.8696
47 S5P 0.8690
48 C2R 0.8660
49 NMN 0.8654
50 CAR 0.8652
51 8OP 0.8543
52 JW5 0.8532
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4L6C; Ligand: 0BT; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 4l6c.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 1L5Y BEF 7.09677
2 1L5Y BEF 7.09677
Pocket No.: 2; Query (leader) PDB : 4L6C; Ligand: 0BT; 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: 4l6c.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
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