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Receptor
PDB id Resolution Class Description Source Keywords
6DW4 1.99 Å EC: 3.1.5.- SAMHD1 BOUND TO CLADRIBINE-TP IN THE CATALYTIC POCKET AND AL POCKET HOMO SAPIENS COMPLEX DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE DNUCLEOTIDE ANALOGUE CLADRIBINE-TP HYDROLASE-HYDROLASE INHCOMPLEX
Ref.: THE STRUCTURAL BASIS FOR CANCER DRUG INTERACTIONS W CATALYTIC AND ALLOSTERIC SITES OF SAMHD1. PROC. NATL. ACAD. SCI. V. 115 10022 2018 U.S.A.
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
HF7 A:705;
D:701;
D:702;
A:703;
C:704;
C:701;
B:701;
B:703;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
505.208 C11 H18 N5 O12 P3 Cc1nc...
NA C:707;
Part of Protein;
none;
submit data
22.99 Na [Na+]
MG A:706;
B:704;
Invalid;
Invalid;
none;
none;
submit data
24.305 Mg [Mg+2...
GTP B:702;
D:703;
A:702;
C:703;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
523.18 C10 H16 N5 O14 P3 c1nc2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6DWD 1.7 Å EC: 3.1.5.- SAMHD1 BOUND TO CLOFARABINE-TP IN THE CATALYTIC POCKET AND A POCKET HOMO SAPIENS COMPLEX DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE DNUCLEOTIDE ANALOGUE CLOFARABINE-TP HYDROLASE HYDROLASE-HINHIBITOR COMPLEX
Ref.: THE STRUCTURAL BASIS FOR CANCER DRUG INTERACTIONS W CATALYTIC AND ALLOSTERIC SITES OF SAMHD1. PROC. NATL. ACAD. SCI. V. 115 10022 2018 U.S.A.
Members (29)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4QFX - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
2 6DW4 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
3 4BZB - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
4 4TO6 - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
5 4RXQ - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
6 6DW7 - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
7 4QFY - DCP C9 H16 N3 O13 P3 C1[C@@H]([....
8 4MZ7 - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
9 4TNX - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
10 4RXP - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
11 4QG4 - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
12 4TO4 - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
13 6DWD - HDV C11 H17 F N5 O12 P3 Cc1nc(c2c(....
14 6DW5 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
15 4ZWG - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
16 4TNZ - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
17 4RXR - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
18 4RXS - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
19 4TO2 - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
20 6DWJ - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
21 6DW3 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
22 4TO3 - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
23 6DWK - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
24 4QG0 - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
25 4TO0 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
26 4QG2 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
27 4QG1 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
28 4TNP - DCP C9 H16 N3 O13 P3 C1[C@@H]([....
29 4QFZ - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
70% Homology Family (29)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4QFX - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
2 6DW4 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
3 4BZB - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
4 4TO6 - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
5 4RXQ - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
6 6DW7 - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
7 4QFY - DCP C9 H16 N3 O13 P3 C1[C@@H]([....
8 4MZ7 - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
9 4TNX - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
10 4RXP - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
11 4QG4 - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
12 4TO4 - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
13 6DWD - HDV C11 H17 F N5 O12 P3 Cc1nc(c2c(....
14 6DW5 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
15 4ZWG - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
16 4TNZ - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
17 4RXR - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
18 4RXS - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
19 4TO2 - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
20 6DWJ - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
21 6DW3 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
22 4TO3 - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
23 6DWK - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
24 4QG0 - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
25 4TO0 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
26 4QG2 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
27 4QG1 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
28 4TNP - DCP C9 H16 N3 O13 P3 C1[C@@H]([....
29 4QFZ - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
50% Homology Family (29)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4QFX - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
2 6DW4 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
3 4BZB - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
4 4TO6 - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
5 4RXQ - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
6 6DW7 - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
7 4QFY - DCP C9 H16 N3 O13 P3 C1[C@@H]([....
8 4MZ7 - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
9 4TNX - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
10 4RXP - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
11 4QG4 - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
12 4TO4 - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
13 6DWD - HDV C11 H17 F N5 O12 P3 Cc1nc(c2c(....
14 6DW5 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
15 4ZWG - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
16 4TNZ - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
17 4RXR - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
18 4RXS - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
19 4TO2 - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
20 6DWJ - DTP C10 H16 N5 O12 P3 c1nc(c2c(n....
21 6DW3 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
22 4TO3 - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
23 6DWK - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
24 4QG0 - DGT C10 H16 N5 O13 P3 c1nc2c(n1[....
25 4TO0 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
26 4QG2 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
27 4QG1 - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
28 4TNP - DCP C9 H16 N3 O13 P3 C1[C@@H]([....
29 4QFZ - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: HF7; Similar ligands found: 30
No: Ligand ECFP6 Tc MDL keys Tc
1 HF7 1 1
2 DTP 0.689655 0.986111
3 HDV 0.655556 0.894737
4 DAT 0.606742 0.986111
5 DGT 0.556701 0.897436
6 HFD 0.520833 0.848101
7 DA 0.511111 0.958333
8 D5M 0.511111 0.958333
9 6OG 0.494737 0.921053
10 DDS 0.484848 0.931507
11 DGI 0.484848 0.897436
12 3AT 0.47 0.918919
13 CL9 0.465909 0.794872
14 2FD 0.460674 0.794872
15 HEJ 0.459184 0.893333
16 ATP 0.459184 0.893333
17 AS 0.457447 0.907895
18 AQP 0.454545 0.893333
19 5FA 0.454545 0.893333
20 7D4 0.44898 0.881579
21 N5P 0.443396 0.7875
22 DOI 0.443299 0.905405
23 6AD 0.436893 0.839506
24 AVV 0.416667 0.873418
25 B4P 0.414141 0.868421
26 AP5 0.414141 0.868421
27 CPA 0.413223 0.851852
28 DCP 0.405941 0.820513
29 BA3 0.40404 0.868421
30 ADP 0.4 0.893333
Ligand no: 2; Ligand: GTP; Similar ligands found: 156
No: Ligand ECFP6 Tc MDL keys Tc
1 GTP 1 1
2 GP3 0.921053 0.973684
3 GDP 0.909091 1
4 GSP 0.853659 0.948718
5 GNH 0.82716 0.986667
6 G1R 0.819277 0.986667
7 GAV 0.811765 0.961039
8 9GM 0.809524 0.973684
9 GNP 0.809524 0.973684
10 GCP 0.797619 0.973684
11 5GP 0.797468 0.986486
12 G 0.797468 0.986486
13 GMV 0.764706 0.973684
14 G2R 0.764045 0.961039
15 G5P 0.755319 0.973684
16 GTG 0.752688 0.936709
17 G2P 0.747126 0.961039
18 G3A 0.744681 0.973684
19 GDD 0.741935 0.961039
20 GDC 0.741935 0.961039
21 GKE 0.741935 0.961039
22 0O2 0.736264 0.986486
23 GP2 0.729412 0.961039
24 6CK 0.726316 0.936709
25 Y9Z 0.723404 0.902439
26 GPG 0.717391 0.961039
27 GFB 0.715789 0.961039
28 GDR 0.715789 0.961039
29 GPD 0.704082 0.925
30 GKD 0.693878 0.961039
31 JB2 0.693878 0.961039
32 GDX 0.686869 0.973684
33 ALF 5GP 0.685393 0.888889
34 GH3 0.681319 0.973333
35 YGP 0.677083 0.901235
36 G3D 0.67033 0.986486
37 GDP AF3 0.659574 0.888889
38 ALF GDP 0.659574 0.888889
39 GDP ALF 0.659574 0.888889
40 DGT 0.659341 0.923077
41 GMP 0.658228 0.88
42 G4P 0.655914 0.986486
43 JB3 0.653846 0.948718
44 NGD 0.647619 0.961039
45 CAG 0.642202 0.880952
46 2MD 0.62963 0.891566
47 MGP 0.619565 0.961039
48 U2G 0.616822 0.936709
49 6G0 0.612903 0.961039
50 MGD 0.612613 0.891566
51 TPG 0.608696 0.840909
52 CG2 0.605505 0.936709
53 GDP 7MG 0.601942 0.911392
54 FEG 0.601852 0.879518
55 G G 0.598039 0.948052
56 ZGP 0.59633 0.869048
57 PGD 0.591304 0.925
58 MD1 0.591304 0.891566
59 3GP 0.590909 0.946667
60 GPX 0.581633 0.946667
61 DGI 0.580645 0.923077
62 IDP 0.576087 0.972973
63 DBG 0.567797 0.948718
64 2GP 0.555556 0.96
65 FE9 0.555556 0.776596
66 G4M 0.547619 0.880952
67 BGO 0.544643 0.924051
68 GCP G 0.543689 0.921053
69 ATP 0.537634 0.92
70 HEJ 0.537634 0.92
71 G1G 0.533898 0.925
72 AQP 0.531915 0.92
73 5FA 0.531915 0.92
74 A G 0.525862 0.935065
75 G A A A 0.525862 0.923077
76 U A G G 0.521368 0.935065
77 HFD 0.520833 0.873418
78 R5I 0.520408 0.946667
79 R7I 0.520408 0.946667
80 01G 0.518868 0.902439
81 P2G 0.510638 0.883117
82 ITT 0.510638 0.868421
83 AKW 0.504348 0.890244
84 GGM 0.504274 0.901235
85 G1R G1R 0.504065 0.924051
86 DGP 0.5 0.910256
87 PGD O 0.5 0.850575
88 MGO 0.5 0.864198
89 DG 0.5 0.910256
90 P1G 0.5 0.871795
91 GTA 0.495495 0.936709
92 PRT 0.490741 0.959459
93 B4P 0.489362 0.894737
94 AP5 0.489362 0.894737
95 IMP 0.489362 0.959459
96 G U 0.487179 0.9
97 7DT 0.484536 0.906667
98 GPC 0.479339 0.879518
99 G C 0.478992 0.9
100 BA3 0.478723 0.894737
101 ADP 0.473684 0.92
102 G2Q 0.471698 0.961039
103 6YZ 0.470588 0.896104
104 G7M 0.46875 0.948052
105 C1Z 0.462963 0.986486
106 25L 0.458716 0.907895
107 A2D 0.457447 0.894737
108 RGT 0.45045 0.909091
109 AGS 0.45 0.873418
110 SAP 0.45 0.873418
111 SGP 0.44898 0.82716
112 A4P 0.445378 0.869048
113 G G G RPC 0.442623 0.875
114 ANP 0.441176 0.896104
115 ACQ 0.441176 0.896104
116 8GT 0.441176 0.875
117 APC G U 0.44 0.886076
118 AT4 0.438776 0.884615
119 G U34 0.438017 0.888889
120 6AD 0.436893 0.841463
121 G G G C 0.433071 0.9125
122 UP5 0.432203 0.873418
123 PCG 0.431373 0.933333
124 C2E 0.431373 0.921053
125 35G 0.431373 0.933333
126 A G C C 0.429688 0.911392
127 T99 0.427184 0.884615
128 5GP 5GP 0.427184 0.883117
129 TAT 0.427184 0.884615
130 AR6 0.425743 0.894737
131 APR 0.425743 0.894737
132 7DD 0.424242 0.906667
133 AN2 0.424242 0.907895
134 DG DG 0.423423 0.865854
135 AD9 0.421569 0.896104
136 M33 0.42 0.883117
137 7D4 0.42 0.835443
138 UCG 0.419847 0.911392
139 HDV 0.419048 0.825
140 H6Y 0.419048 0.946667
141 G C C C 0.416667 0.924051
142 ACP 0.415842 0.896104
143 T5A 0.414634 0.802326
144 A1R 0.412844 0.839506
145 ADQ 0.412844 0.871795
146 MGQ 0.412844 0.935897
147 A3R 0.412844 0.839506
148 MGT 0.411215 0.823529
149 A G U 0.410072 0.888889
150 93A 0.41 0.833333
151 A22 0.407407 0.907895
152 CA0 0.405941 0.896104
153 ATF 0.40566 0.884615
154 AGO 0.404762 0.888889
155 MGV 0.401786 0.890244
156 CGP 0.4 0.86747
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6DWD; Ligand: HDV; Similar sites found with APoc: 14
This union binding pocket(no: 1) in the query (biounit: 6dwd.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 2JCB ADP 2.5
2 1YVZ JPC 2.90909
3 3GWT 066 4.24929
4 4S1B 2BA 4.5045
5 5BU2 RIB 5.28634
6 4AVV CD 5.39216
7 4AVV GHE 5.39216
8 1XON PIL 6.01719
9 1U3G ADP 11.1111
10 5ZCO CHD 13.6054
11 5Z84 CHD 13.6054
12 5W97 CHD 13.6054
13 4J6W C 19.5122
14 4N6W FLC 39.9123
Pocket No.: 2; Query (leader) PDB : 6DWD; Ligand: HDV; Similar sites found with APoc: 20
This union binding pocket(no: 2) in the query (biounit: 6dwd.bio1) has 63 residues
No: Leader PDB Ligand Sequence Similarity
1 1SDW IYT 3.50318
2 3P48 DUP 4.08163
3 1Y2W NAG 4.22535
4 3UEC ALA ARG TPO LYS 4.79452
5 4Z2S NDG 4.92958
6 4Z2S NAG 4.92958
7 2OFE NAG 4.92958
8 2OFD NGA 4.92958
9 1JOC ITP 5.6
10 4TVD BGC 6.72727
11 5N6N SUC 7.91667
12 3QDV NDG 9.09091
13 3QDU CBS CBS 9.09091
14 3QX9 ATP 12.3188
15 5EB3 UEG 13.2075
16 4LRL TTP 21.0417
17 4LRL DGT 21.0417
18 5E6O TRP GLU GLU LEU 22.0339
19 1PVC ILE SER GLU VAL 27.9412
20 2HEK GDP 36.9272
Pocket No.: 3; Query (leader) PDB : 6DWD; Ligand: HDV; Similar sites found with APoc: 1
This union binding pocket(no: 3) in the query (biounit: 6dwd.bio1) has 62 residues
No: Leader PDB Ligand Sequence Similarity
1 2Y91 98J 2.26415
Pocket No.: 4; Query (leader) PDB : 6DWD; Ligand: GTP; Similar sites found with APoc: 16
This union binding pocket(no: 4) in the query (biounit: 6dwd.bio1) has 62 residues
No: Leader PDB Ligand Sequence Similarity
1 2Y91 98J 2.26415
2 1SDW IYT 3.50318
3 3P48 DUP 4.08163
4 3UEC ALA ARG TPO LYS 4.79452
5 4Z2S NAG 4.92958
6 4Z2S NDG 4.92958
7 2OFE NAG 4.92958
8 2OFD NGA 4.92958
9 1JOC ITP 5.6
10 5N6N SUC 7.91667
11 3QDV NDG 9.09091
12 3QX9 ATP 12.3188
13 4LRL TTP 21.0417
14 4LRL DGT 21.0417
15 1PVC ILE SER GLU VAL 27.9412
16 2HEK GDP 36.9272
Pocket No.: 5; Query (leader) PDB : 6DWD; Ligand: HDV; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 6dwd.bio1) has 62 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 6DWD; Ligand: HDV; Similar sites found with APoc: 6
This union binding pocket(no: 6) in the query (biounit: 6dwd.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 6CGN DA 2.54545
2 4UMJ BFQ 3.04054
3 5VRH OLB 3.63985
4 4K10 NI9 6.07735
5 1SWG BTN 7.03125
6 4WH9 3M8 7.65027
Pocket No.: 7; Query (leader) PDB : 6DWD; Ligand: HDV; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 6dwd.bio1) has 62 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 6DWD; Ligand: HDV; Similar sites found with APoc: 3
This union binding pocket(no: 8) in the query (biounit: 6dwd.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 1B09 PC 4.36893
2 4I90 CHT 9.90099
3 6FC1 MGP 14.0625
Pocket No.: 9; Query (leader) PDB : 6DWD; Ligand: GTP; Similar sites found with APoc: 5
This union binding pocket(no: 9) in the query (biounit: 6dwd.bio1) has 62 residues
No: Leader PDB Ligand Sequence Similarity
1 1Y2W NAG 4.22535
2 4TVD BGC 6.72727
3 3QDU CBS CBS 9.09091
4 5EB3 UEG 13.2075
5 5E6O TRP GLU GLU LEU 22.0339
Pocket No.: 10; Query (leader) PDB : 6DWD; Ligand: HDV; Similar sites found with APoc: 4
This union binding pocket(no: 10) in the query (biounit: 6dwd.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 3LGS SAH 2.24719
2 4WBD CIT 4.06654
3 6D5V FVY 9.58084
4 6D5J FV4 9.58084
Pocket No.: 11; Query (leader) PDB : 6DWD; Ligand: GTP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 11) in the query (biounit: 6dwd.bio1) has 62 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 12; Query (leader) PDB : 6DWD; Ligand: GTP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 12) in the query (biounit: 6dwd.bio1) has 62 residues
No: Leader PDB Ligand Sequence Similarity
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