Receptor
PDB id Resolution Class Description Source Keywords
2CVY 2.4 Å EC: 1.17.4.1 STRUCTURES OF YEAST RIBONUCLEOTIDE REDUCTASE I SACCHAROMYCES CEREVISIAE EUKARYOTIC RIBONUCLEOTIDE REDUCTASE DNTP REGULATION OXIDOREDUCTASE
Ref.: STRUCTURES OF EUKARYOTIC RIBONUCLEOTIDE REDUCTASE I PROVIDE INSIGHTS INTO DNTP REGULATION PROC.NATL.ACAD.SCI.USA V. 103 4022 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GLY ALA PHE THR PHE ASN GLU ASP PHE B:3;
 Valid;
 none;
 submit data
915.934 n/a O=C([...
MG A:2001;
 Invalid;
 none;
 submit data
24.305 Mg [Mg+2...
TTP A:1001;
 Valid;
 none;
 submit data
482.168 C10 H17 N2 O14 P3 CC1=C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3RSR 2.3 Å EC: 1.17.4.1 CRYSTAL STRUCTURE OF 5-NITP INHIBITION OF YEAST RIBONUCLEOTI REDUCTASE SACCHAROMYCES CEREVISIAE 10-STRANDED ALPHA/BETA BARREL NUCLEOTIDE REDUCTION OXIDIZEOXIDOREDUCTASE
Ref.: EVALUATING THE THERAPEUTIC POTENTIAL OF A NON-NATUR NUCLEOTIDE THAT INHIBITS HUMAN RIBONUCLEOTIDE REDUC MOL.CANCER THER. V. 11 2077 2012
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 11 families.
1 3RSR Kd = 44 uM N5P C13 H17 N2 O14 P3 c1cc2c(ccn....
2 3K8T - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
3 2CVY - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
4 2CVW - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
5 2CVX - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
6 2EUD - GCQ C9 H13 F2 N3 O10 P2 C1=CN(C(=O....
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 3RSR Kd = 44 uM N5P C13 H17 N2 O14 P3 c1cc2c(ccn....
2 3K8T - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
3 2CVY - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
4 2CVW - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
5 2CVX - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
6 2EUD - GCQ C9 H13 F2 N3 O10 P2 C1=CN(C(=O....
7 2WGH - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
8 3HNC - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 3RSR Kd = 44 uM N5P C13 H17 N2 O14 P3 c1cc2c(ccn....
2 3K8T - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
3 2CVY - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
4 2CVW - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
5 2CVX - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
6 2EUD - GCQ C9 H13 F2 N3 O10 P2 C1=CN(C(=O....
7 2WGH - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
8 3HNC - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GLY ALA PHE THR PHE ASN GLU ASP PHE; Similar ligands found: 119
No: Ligand ECFP6 Tc MDL keys Tc
1 GLY ALA PHE THR PHE ASN GLU ASP PHE 1 1
2 ACE ASN TRP GLU THR PHE 0.586207 0.849057
3 THR ASN GLU PHE TYR PHE 0.585859 0.893617
4 ALA GLU THR PHE 0.578947 0.869565
5 ASP ALA ASP GLU GLU ASP PHE 0.575758 0.808511
6 THR ASN GLU PHE TYR ALA 0.564815 0.9375
7 TYR GLN GLU SER THR ASP PHE THR PHE LEU 0.563107 0.854167
8 ILE ASN PHE ASP PHE ASN THR ILE 0.556604 0.916667
9 THR ASN GLU PHE ALA PHE 0.554455 0.888889
10 VAL ASN ASP ILE PHE GLU ALA ILE 0.542373 0.816327
11 ASP ASN ARG LEU GLY LEU VAL TYR GLN PHE 0.537037 0.8
12 CYS THR GLU LEU LYS LEU ASN ASP TYR 0.536585 0.767857
13 GLU GLU TYR LEU GLN ALA PHE THR TYR 0.528 0.843137
14 SER GLY ILE PHE LEU GLU THR SER 0.522124 0.788462
15 GLU ASN GLN LYS GLU TYR PHE PHE 0.522124 0.792453
16 LEU ASP GLU GLU THR GLY GLU PHE LEU 0.521008 0.773585
17 GLU GLU ASN LEU LEU ASP PHE VAL ARG PHE 0.51938 0.724138
18 THR PHE LYS LYS THR ASN 0.513761 0.807692
19 SER PHE PHE GLU ASP ASN PHE VAL PRO GLU 0.512 0.6875
20 GLY ALA GLU THR PHE TYR VAL ASP GLY ALA 0.512 0.814815
21 ALA GLU THR PHE TYR VAL ASP GLY 0.508621 0.897959
22 ASP PHE GLU GLU ILE 0.5 0.734694
23 ACE PHE ASP GLU MET GLU GLU CYS 0.5 0.654545
24 ASP PHE GLU ASP TYR GLU PHE ASP 0.5 0.84
25 GLU ILE ILE ASN PHE GLU LYS LEU 0.491935 0.690909
26 SER ILE ILE ASN PHE GLU LYS LEU 0.488 0.745455
27 GLY ALA GLN THR PHE TYR VAL ASP GLY ALA 0.487805 0.830189
28 THR GLU ASN LEU TYR PHE GLN SER GLY THR 0.484848 0.803571
29 LEU ARG ASN GLN SER VAL PHE ASN PHE 0.484375 0.745763
30 GLY ILE LEU GLU PHE VAL PHE THR LEU 0.483607 0.807692
31 ALA VAL TYR ASN PHE ALA THR MET 0.48 0.8
32 CYS THR PHE LYS THR LYS THR ASN 0.478261 0.792453
33 GLU VAL ASN 1OL ALA GLU PHE 0.476562 0.8
34 GLU THR PHE TYR VAL ASP GLY 0.475 0.830189
35 ASN GLN LEU ALA TRP PHE ASP THR ASP LEU 0.474453 0.814815
36 ACE MET GLU GLU VAL PHE 0.472222 0.618182
37 ALA SER ASN GLU ASP MET GLU THR MET 0.469027 0.727273
38 ASP PHE GLN GLU SER ALA ASP SER PHE LEU 0.467742 0.826923
39 GLU LEU ASP 1OL VAL GLU PHE 0.464567 0.76
40 GLY ALA GLU VAL PHE TYR VAL ASP GLY ALA 0.464 0.759259
41 PRO GLU SEP LEU GLU SER CYS PHE 0.46281 0.666667
42 THR ASN GLU TYR TYR VAL 0.462264 0.877551
43 SER GLU ASP GLU PHE TYR ASP ALA LEU SER 0.461538 0.796296
44 CYS THR GLU LEU LYS LEU SER ASP TYR 0.461538 0.736842
45 THR LYS ASN TYR LYS GLN THR SER VAL 0.457364 0.767857
46 PHE GLU ASP LEU ARG LEU LEU SER PHE 0.456693 0.711864
47 GLU THR LEU GLU ASP SER VAL PHE 0.456311 0.76
48 ACE VAL PHE PHE ALA GLU ASP NH2 0.455357 0.808511
49 PHE GLU ASP LEU ARG VAL LEU SER PHE 0.455224 0.711864
50 PHE GLU ASP LEU ARG VAL SER SER PHE 0.455224 0.711864
51 GLU ASN LEU TYR PHE GLN 0.453782 0.843137
52 LYS PRO ILE VAL GLN TYR ASP ASN PHE 0.452703 0.647059
53 ALA THR PRO PHE GLN GLU 0.452381 0.639344
54 ALA THR ARG ASN PHE SER GLY 0.451613 0.706897
55 ACE GLU ASN LEU TYR PHE GLN SER GLY THR 0.451613 0.826923
56 GLU ASP GLU ASP PHE GLU ILE LEU SER LEU 0.450382 0.773585
57 TRP ASN TRP PHE ASP ILE THR ASN LYS 0.449275 0.8
58 SER LEU PHE ASN THR VAL ALA THR LEU 0.448 0.784314
59 SER SER LEU GLU ASN PHE ALA ALA TYR VAL 0.447761 0.849057
60 CYS ASP PTR ALA ASN PHE LYS 0.447619 0.76
61 ARG PRO GLY ASN PHE PHE GLN ASN ARG PRO 0.447368 0.764706
62 ALA SER ASN GLU ASN TRP GLU THR MET 0.44697 0.721311
63 ARG GLU ASP GLN GLU THR ALA VAL 0.446429 0.791667
64 THR LYS ASN TYR LYS GLN PHE SER VAL 0.444444 0.818182
65 ALA LEU ASP LEU PHE 0.444444 0.708333
66 PRO ALA TRP ASP GLU THR ASN LEU 0.443662 0.721311
67 ACE SER LEU ASN PHE 0.443396 0.75
68 LYS VAL ILE THR PHE ILE ASP LEU 0.440945 0.759259
69 ASP PHE M3L THR ASP 0.440678 0.688525
70 GLU ASP GLU ASP PHE GLU ILE LEU SEP LEU 0.438849 0.633333
71 GLN PHE LYS ASP ASN VAL ILE LEU LEU 0.437037 0.740741
72 LYS MET ASN THR GLN PHE THR ALA VAL 0.437037 0.724138
73 THR ASN GLU TYR LYS VAL 0.435897 0.759259
74 ALA SER ASN GLU ASN MET GLU THR MET 0.433628 0.727273
75 SER HIS PHE ASN GLU TYR GLU 0.432836 0.758621
76 ASP GLU ASP LYS TRP ASP ASP PHE 0.432 0.696429
77 LYS ALA VAL PHE ASN PHE ALA THR MET 0.432 0.773585
78 VAL GLN GLN GLU SER SER PHE VAL MET 0.430894 0.714286
79 TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 0.430657 0.677419
80 GLU GLU GLN GLU GLU TYR 0.43 0.770833
81 FME TYR PHE ILE ASN ILE LEU THR LEU 0.42963 0.803571
82 VAL VAL SER HIS PHE ASN ASP 0.428571 0.736842
83 GLU GLU TYR LEU LYS ALA TRP THR PHE 0.427632 0.693548
84 LYS ALA VAL TYR ASN PHE ALA THR MET 0.427481 0.763636
85 ACE THR GLU ASP VAL VAL CYS CYS 0.427273 0.74
86 ARG ABA GLN ILE PHE ALA ASN ILE 0.426357 0.730769
87 ASP PHE 0.423913 0.711111
88 ILE THR ASP GLN VAL PRO PHE SER VAL 0.423611 0.621212
89 ACE GLN ALC ASP LEU PHE 0.422764 0.698113
90 GLU THR VAL ARG PHE GLN SER ASP 0.422222 0.689655
91 LEU GLU PHE GLN GLY 0.421053 0.660377
92 SER GLN ASN TYR 0.420561 0.84
93 MET ASN GLU ASN ILE 0.42 0.770833
94 TYR GLN PHE 0.419048 0.829787
95 GLU PRO VAL GLU THR THR ASP TYR 0.41791 0.65625
96 ALA ILE PHE GLN SER SER MET THR LYS 0.41791 0.694915
97 ALA THR ALA ALA ALA THR GLU ALA TYR 0.417391 0.875
98 ARG ARG GLU VAL HIS THR TYR TYR 0.415493 0.692308
99 ASP ALA ASP GLU TYR LEU 0.415254 0.8
100 GLN MET PRO THR GLU ASP GLU TYR 0.412587 0.608696
101 ALA SER ASN GLU HIS MET GLU THR MET 0.412214 0.677419
102 ALA SER ASN GLU ASN ALA GLU THR MET 0.408333 0.727273
103 GLY TYR GLU ASN PRO THR TYR LYS PHE PHE 0.407895 0.703125
104 PRO GLU GLY ASP PM3 GLU GLU VAL LEU 0.407692 0.616667
105 SER ILE ILE GLN PHE GLU HIS LEU 0.407407 0.7
106 TYR GLU TRP 0.405172 0.735849
107 GLY ASP GLU VAL LYS VAL PHE ARG 0.404412 0.6
108 ASP PHE ALA ASN THR PHE LEU PRO 0.404412 0.714286
109 GLU GLU PHE GLY ARG ALA PHE SER PHE 0.404412 0.719298
110 MET ASN TYR ASP ILE 0.403846 0.74
111 ALA SER ASN GLU ASN ILE GLU THR MET 0.401639 0.714286
112 SER LEU PHE ASN THR VAL ALA THR LEU TYR 0.40146 0.792453
113 LEU PRO SER PHE GLU THR ALA LEU 0.4 0.630769
114 ILE ASP TRP PHE ASP GLY LYS GLU 0.4 0.666667
115 ILE ASP TRP PHE GLU GLY LYS GLU 0.4 0.639344
116 ALA ASN SER ARG TRP GLN ASP THR ARG LEU 0.4 0.666667
117 GLU GLN TYR LYS PHE TYR SER VAL 0.4 0.767857
118 PHE LEU 0.4 0.625
119 LYS LYS ALA THR GLN ALA SEP GLN GLU TYR 0.4 0.706897
Ligand no: 2; Ligand: TTP; Similar ligands found: 84
No: Ligand ECFP6 Tc MDL keys Tc
1 TTP 1 1
2 TYD 0.884058 1
3 TMP 0.760563 0.985714
4 TLO 0.722892 0.945205
5 DAU 0.701149 0.932432
6 TRH 0.689655 0.932432
7 1JB 0.689655 0.932432
8 TDX 0.689655 0.945205
9 3R2 0.689655 0.92
10 18T 0.689655 0.932432
11 T3Q 0.674157 0.907895
12 3YN 0.674157 0.932432
13 DWN 0.674157 0.907895
14 T3F 0.674157 0.907895
15 0N2 0.666667 0.896104
16 T46 0.666667 0.932432
17 0FX 0.659341 0.907895
18 MMF 0.659341 0.907895
19 TTP MG 0.646341 0.943662
20 QDM 0.645161 0.896104
21 FNF 0.638298 0.92
22 JHZ 0.638298 0.884615
23 1YF 0.638298 0.92
24 AKM 0.638298 0.886076
25 9RC 0.636364 0.829268
26 4TG 0.631579 0.92
27 DUT 0.62963 0.957143
28 TBD 0.62963 0.958904
29 D3T 0.62963 0.971831
30 T5A 0.61165 0.841463
31 LLT 0.605634 0.873239
32 THM 0.605634 0.873239
33 ATY 0.6 0.945205
34 FUH 0.588235 0.907895
35 QUH 0.588235 0.907895
36 AZD 0.586207 0.907895
37 UFP 0.56962 0.905405
38 0DN 0.567568 0.833333
39 DCP 0.55814 0.891892
40 BRU 0.54321 0.905405
41 5HU 0.54321 0.971831
42 DUD 0.542169 0.957143
43 NYM 0.536585 0.958333
44 FDM 0.536585 0.918919
45 5IU 0.536585 0.905405
46 F6G 0.534091 0.855263
47 ABT 0.531915 0.884615
48 T3P 0.531646 0.943662
49 THP 0.53012 0.971429
50 D4T 0.528736 0.928571
51 6U4 0.521277 0.848101
52 ATM 0.517241 0.894737
53 TQP 0.512605 0.864198
54 7SG 0.512605 0.864198
55 TXS 0.512195 0.789474
56 TPE 0.510204 0.894737
57 T4K 0.508333 0.853659
58 T5K 0.508333 0.853659
59 3DR DT DT DT DT DT 0.504854 0.905405
60 BVP 0.5 0.944444
61 T3S 0.5 0.789474
62 8DG 0.489583 0.829268
63 BUP 0.477778 0.842105
64 YYY 0.477273 0.891892
65 2DT 0.47561 0.957747
66 4TA 0.469565 0.807229
67 DT ME6 DT 0.468468 0.87013
68 D4D 0.449438 0.928571
69 DU 0.447059 0.942857
70 UMP 0.447059 0.942857
71 AZZ 0.447059 0.779221
72 523 0.442105 0.921053
73 5CM 0.438202 0.918919
74 DUP 0.430108 0.930556
75 ADS THS THS THS 0.429752 0.758621
76 UTP 0.428571 0.875
77 8DD 0.424242 0.8125
78 U5F 0.423913 0.875
79 WMJ 0.42 0.761905
80 DDN 0.418605 0.942857
81 8GD 0.418367 0.829268
82 DGT 0.415842 0.759036
83 UC5 0.406593 0.943662
84 ID2 0.402439 0.8
Similar Ligands (3D)
Ligand no: 1; Ligand: GLY ALA PHE THR PHE ASN GLU ASP PHE; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 2; Ligand: TTP; Similar ligands found: 28
No: Ligand Similarity coefficient
1 DTP 0.9873
2 DZ4 0.9766
3 MG TTP 0.9753
4 HF7 0.9630
5 HEJ 0.9540
6 HDV 0.9485
7 HF4 0.9432
8 DUT MG 0.9338
9 HFD 0.9332
10 JSQ 0.9100
11 GTF 0.9093
12 ACP 0.9066
13 ANP 0.9060
14 CTP 0.8971
15 AGS 0.8934
16 ATP 0.8917
17 3AT 0.8877
18 GTP 0.8866
19 2KH 0.8825
20 0RC 0.8807
21 DCT 0.8752
22 APC 0.8740
23 MGT 0.8701
24 SAM 0.8585
25 UDP 0.8581
26 ADP BEF 0.8567
27 GNP 0.8526
28 ADP ALF 0.8523
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3RSR; Ligand: N5P; 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: 3rsr.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3RSR; Ligand: N5P; 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: 3rsr.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
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