Receptor
PDB id Resolution Class Description Source Keywords
1Z4K 1.75 Å EC: 3.1.3.5 STRUCTURE OF THE D41N VARIANT OF THE HUMAN MITOCHONDRIAL DEOXYRIBONUCLEOTIDASE IN COMPLEX WITH THYMIDINE 3'- M ONOPHOSPHATE HOMO SAPIENS ALFA BETA FOLD HYDROLASE
Ref.: STRUCTURAL BASIS FOR SUBSTRATE SPECIFICITY OF THE HUMAN MITOCHONDRIAL DEOXYRIBONUCLEOTIDASE STRUCTURE V. 13 1081 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:229;
 Part of Protein;
 none;
 submit data
24.305 Mg [Mg+2...
T3P A:4341;
 Valid;
 none;
 submit data
322.208 C10 H15 N2 O8 P CC1=C...
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: T3P; Similar ligands found: 56
No: Ligand ECFP6 Tc MDL keys Tc
1 T3P 1 1
2 THP 0.753846 0.971014
3 LLT 0.629032 0.84507
4 THM 0.629032 0.84507
5 TMP 0.6 0.957143
6 UM3 0.573529 0.955882
7 FDM 0.569444 0.917808
8 NYM 0.569444 0.930556
9 0DN 0.560606 0.805556
10 TYD 0.56 0.943662
11 ATY 0.556962 0.917808
12 AZZ 0.549296 0.824324
13 TBD 0.545455 0.905405
14 TTP 0.531646 0.943662
15 ATM 0.525641 0.893333
16 AZD 0.506024 0.881579
17 2DT 0.5 0.957143
18 TXS 0.5 0.763158
19 TTP MG 0.487805 0.915493
20 T3S 0.486842 0.763158
21 DAU 0.483516 0.905405
22 TPE 0.483516 0.868421
23 3DR DT DT DT DT DT 0.479167 0.878378
24 TLO 0.477273 0.891892
25 9RC 0.47191 0.804878
26 3YN 0.462366 0.88
27 18T 0.456522 0.88
28 1JB 0.456522 0.88
29 TRH 0.456522 0.88
30 3R2 0.456522 0.868421
31 TDX 0.456522 0.891892
32 ABT 0.455556 0.858974
33 D3T 0.451219 0.943662
34 DWN 0.446809 0.857143
35 T3Q 0.446809 0.857143
36 T3F 0.446809 0.857143
37 0N2 0.442105 0.846154
38 T46 0.442105 0.88
39 0FX 0.4375 0.857143
40 MMF 0.4375 0.857143
41 DT ME6 DT 0.428571 0.844156
42 QDM 0.428571 0.846154
43 ADS THS THS THS 0.428571 0.755814
44 FNF 0.424242 0.868421
45 JHZ 0.424242 0.835443
46 AKM 0.424242 0.8375
47 1YF 0.424242 0.868421
48 DPB 0.423529 0.902778
49 PAX 0.422414 0.82716
50 4TG 0.42 0.868421
51 5HU 0.417722 0.943662
52 D4M 0.410256 0.913043
53 UFP 0.405063 0.878378
54 0BT 0.404494 0.855263
55 WMJ 0.402174 0.738095
56 BRU 0.4 0.878378
Similar Ligands (3D)
Ligand no: 1; Ligand: T3P; Similar ligands found: 67
No: Ligand Similarity coefficient
1 U3P 0.9522
2 101 0.9498
3 C3P 0.9417
4 UA3 0.9279
5 103 0.9245
6 3AM 0.9189
7 UMF 0.9161
8 A3G 0.9156
9 3GP 0.9095
10 ACK 0.9095
11 QQX 0.9039
12 U2P 0.9038
13 UVC 0.9003
14 C2P 0.8995
15 SGP 0.8971
16 2AM 0.8965
17 2GP 0.8927
18 M0Y 0.8890
19 OVE 0.8883
20 IGP 0.8869
21 VM7 0.8863
22 IAG 0.8855
23 1FL 0.8818
24 D5M 0.8813
25 UMP 0.8797
26 G 0.8746
27 XTS 0.8715
28 BK2 0.8703
29 0DJ 0.8698
30 1SF 0.8697
31 ADN 0.8697
32 AMP 0.8690
33 ZAS 0.8685
34 4OZ 0.8682
35 GMP 0.8675
36 RVC 0.8671
37 6MA 0.8656
38 XEV 0.8653
39 21E 0.8650
40 M0Z 0.8642
41 Q4G 0.8636
42 MTA 0.8635
43 5BX 0.8633
44 AQ1 0.8625
45 8OG 0.8617
46 Y3J 0.8617
47 PY1 0.8617
48 MCY 0.8607
49 FX5 0.8605
50 A3S 0.8601
51 EAE 0.8593
52 28B 0.8590
53 3AD 0.8589
54 6F3 0.8583
55 AV4 0.8569
56 U4J 0.8563
57 Q92 0.8561
58 C5P 0.8561
59 KWV 0.8559
60 AUV 0.8555
61 TVC 0.8549
62 ID2 0.8546
63 AGV 0.8542
64 JMQ 0.8542
65 7VF 0.8542
66 EZN 0.8542
67 MBY 0.8531
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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