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Receptor
PDB id Resolution Class Description Source Keywords
4KXN 1.9 Å EC: 3.2.2.- CRYSTAL STRUCTURE OF DNPH1 (RCL) WITH KINETINE RIBOSIDE MONO RATTUS NORVEGICUS DEOXYRIBONUCLEOSIDE 5-prime -MONOPHOSPHATE N-GLYCOSIDASE HYDROLAS
Ref.: N (6)-SUBSTITUTED AMPS INHIBIT MAMMALIAN DEOXYNUCLE N-HYDROLASE DNPH1. PLOS ONE V. 8 80755 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
6K6 B:201;
D:201;
A:201;
C:201;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Ki = 1.8 uM
427.306 C15 H18 N5 O8 P c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4KXL 1.69 Å EC: 3.2.2.- CRYSTAL STRUCTURE OF DNPH1 (RCL) WITH 6-CYCLOPENTYL-AMP RATTUS NORVEGICUS DEOXYRIBONUCLEOSIDE 5-prime -MONOPHOSPHATE N-GLYCOSIDASE HYDROLAS
Ref.: N (6)-SUBSTITUTED AMPS INHIBIT MAMMALIAN DEOXYNUCLE N-HYDROLASE DNPH1. PLOS ONE V. 8 80755 2013
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 4P5D Ki = 1.5 uM N6P C20 H19 N4 O7 P c1ccc2cc(c....
2 4KXM Ki = 3.3 uM 6IA C15 H24 N5 O7 P CC(C)CCNc1....
3 4KXL Ki = 1.2 uM 6C6 C15 H22 N5 O7 P c1nc(c2c(n....
4 4KXN Ki = 1.8 uM 6K6 C15 H18 N5 O8 P c1cc(oc1)C....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 4P5D Ki = 1.5 uM N6P C20 H19 N4 O7 P c1ccc2cc(c....
2 4KXM Ki = 3.3 uM 6IA C15 H24 N5 O7 P CC(C)CCNc1....
3 4KXL Ki = 1.2 uM 6C6 C15 H22 N5 O7 P c1nc(c2c(n....
4 4KXN Ki = 1.8 uM 6K6 C15 H18 N5 O8 P c1cc(oc1)C....
5 4P5E Ki = 2.8 uM N6P C20 H19 N4 O7 P c1ccc2cc(c....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4P5D Ki = 1.5 uM N6P C20 H19 N4 O7 P c1ccc2cc(c....
2 4KXM Ki = 3.3 uM 6IA C15 H24 N5 O7 P CC(C)CCNc1....
3 4KXL Ki = 1.2 uM 6C6 C15 H22 N5 O7 P c1nc(c2c(n....
4 4KXN Ki = 1.8 uM 6K6 C15 H18 N5 O8 P c1cc(oc1)C....
5 4P5E Ki = 2.8 uM N6P C20 H19 N4 O7 P c1ccc2cc(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 6K6; Similar ligands found: 95
No: Ligand ECFP6 Tc MDL keys Tc
1 6K6 1 1
2 6IA 0.666667 0.896104
3 6C6 0.585106 0.893333
4 2SA 0.56701 0.893333
5 AMP 0.539326 0.957143
6 A 0.539326 0.957143
7 IMO 0.521739 0.915493
8 N6P 0.476636 0.928571
9 ITT 0.464646 0.902778
10 PGS 0.464646 0.846154
11 AU1 0.464646 0.905405
12 50T 0.46 0.917808
13 ADP 0.459184 0.930556
14 A2D 0.458333 0.90411
15 ABM 0.458333 0.90411
16 25A 0.457944 0.930556
17 APC 0.455446 0.893333
18 6MD 0.449438 0.819444
19 A12 0.44898 0.893333
20 AP2 0.44898 0.893333
21 BA3 0.44898 0.90411
22 71V 0.44898 0.87013
23 HEJ 0.445545 0.930556
24 ATP 0.445545 0.930556
25 ACP 0.445545 0.905405
26 B4P 0.444444 0.90411
27 AP5 0.444444 0.90411
28 ACQ 0.442308 0.905405
29 5FA 0.441176 0.930556
30 AQP 0.441176 0.930556
31 AN2 0.44 0.917808
32 AT4 0.44 0.893333
33 SRA 0.4375 0.905405
34 M33 0.435644 0.891892
35 CA0 0.435644 0.88
36 ADX 0.435644 0.814815
37 36A 0.433333 0.710843
38 6YZ 0.429907 0.905405
39 WAQ 0.428571 0.846154
40 TAT 0.428571 0.893333
41 T99 0.428571 0.893333
42 ANP 0.428571 0.905405
43 PRX 0.427184 0.88
44 APR 0.427184 0.90411
45 AR6 0.427184 0.90411
46 1RB 0.427083 0.898551
47 C2R 0.425532 0.84
48 1ZZ 0.424779 0.804878
49 FYA 0.424779 0.891892
50 5AL 0.424528 0.891892
51 AHX 0.423423 0.858974
52 DLL 0.423423 0.891892
53 ADV 0.423077 0.868421
54 RBY 0.423077 0.868421
55 AGS 0.423077 0.881579
56 SAP 0.423077 0.881579
57 AD9 0.423077 0.905405
58 ATF 0.420561 0.893333
59 7RP 0.418367 0.942029
60 9ZA 0.418182 0.87013
61 9ZD 0.418182 0.87013
62 OOB 0.418182 0.891892
63 AIR 0.417582 0.887324
64 SRP 0.416667 0.893333
65 GAP 0.415094 0.905405
66 4AD 0.414414 0.857143
67 AMO 0.414414 0.868421
68 RMB 0.414141 0.885714
69 JLN 0.414141 0.851351
70 NB8 0.412281 0.835443
71 PTJ 0.412281 0.858974
72 ARU 0.410714 0.848101
73 AMZ 0.410526 0.851351
74 ADP PO3 0.409524 0.902778
75 MAP 0.409091 0.881579
76 A22 0.409091 0.917808
77 ADP ALF 0.407407 0.833333
78 ALF ADP 0.407407 0.833333
79 3UK 0.40708 0.88
80 AMP DBH 0.40678 0.855263
81 8QN 0.405405 0.891892
82 5SV 0.405405 0.835443
83 LAD 0.403509 0.871795
84 B5V 0.403509 0.868421
85 NIA 0.402062 0.7875
86 ADQ 0.401786 0.905405
87 PAJ 0.401786 0.848101
88 A1R 0.401786 0.894737
89 A3R 0.401786 0.894737
90 FA5 0.401709 0.868421
91 7RA 0.4 0.943662
92 AAM 0.4 0.957143
93 P2P 0.4 0.915493
94 BIS 0.4 0.87013
95 FAI 0.4 0.851351
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4KXL; Ligand: 6C6; Similar sites found with APoc: 122
This union binding pocket(no: 1) in the query (biounit: 4kxl.bio2) has 48 residues
No: Leader PDB Ligand Sequence Similarity
1 4RJD TFP None
2 2VWA PTY None
3 1S2D ADE None
4 4ZGM 32M None
5 1KJ1 MAN None
6 3RV5 DXC None
7 5N8V KZZ None
8 1WUW TSU None
9 4NTO 1PW 1.31579
10 3L8G GMB 1.31579
11 6EK3 OUL 1.35747
12 2CIX CEJ 1.97368
13 3GLC R5P 1.97368
14 5OSW DIU 1.97368
15 1U6R IOM 2.63158
16 4I90 CHT 2.63158
17 4OB6 S2T 2.63158
18 3K0T BGC 2.7972
19 5YRL GLC GLC 2.8169
20 5YRJ BGC GLC 2.8169
21 5YRM BGC GLC 2.8169
22 5DQY BEZ 2.85714
23 1NU4 MLA 3.09278
24 4JEJ 1GP 3.28947
25 3O7J 2AL 3.28947
26 5YSI NCA 3.28947
27 1C9K 5GP 3.28947
28 1M2Z BOG 3.94737
29 5UGW GSH 3.94737
30 5XLA SIA 3.94737
31 3KC1 2T6 3.94737
32 1GXS BEZ 3.94737
33 5A3Y VAL LYS 3.94737
34 3HQP FDP 3.94737
35 5CXX FER 3.94737
36 2B56 U5P 3.94737
37 2BVE PH5 4.20168
38 6F9G PUT 4.36137
39 4JLS 3ZE 4.60526
40 6E1Q CFA 4.60526
41 2PNC CLU 4.60526
42 2Q37 3AL 4.60526
43 2EB5 OXL 4.60526
44 1BO4 COA 4.60526
45 4CUB GAL NAG 4.60526
46 3EXS 5RP 4.60526
47 5VLQ ANP 4.60526
48 4SGA ACE PRO ALA PRO PHE 4.60526
49 4G86 BNT 5.26316
50 3B9Z CO2 5.26316
51 5TED SKM 5.26316
52 3E70 GDP 5.26316
53 5N26 CPT 5.26316
54 3GD8 GOL 5.26316
55 1SW0 PGA 5.26316
56 5LB3 ADP 5.26316
57 3ITJ CIT 5.26316
58 2IYG FMN 5.64516
59 4OHB 5HM 5.92105
60 3E7S AT2 5.92105
61 3QH2 3NM 5.92105
62 5J32 IPM 5.92105
63 1CT9 GLN 5.92105
64 1L7N ALF 5.92105
65 5YJS SAL 5.92105
66 5H3A D16 5.92105
67 3LN9 FLC 6.47482
68 5LX9 OLB 6.57895
69 4ZQX ATP 6.57895
70 4GYS MLI 6.57895
71 5WBF LAC 6.57895
72 5AWV GHP 3MY 3FG GHP GHP OMY 3FG NAG MAN 6.57895
73 4A8T PAO 6.57895
74 5TQZ GLC 6.66667
75 3KO0 TFP 6.93069
76 4MZU TDR 7.23684
77 5W6Y TRP 7.23684
78 3R75 PYR 7.23684
79 1T36 ORN 7.23684
80 5W7B MYR 7.80142
81 1WLJ U5P 7.89474
82 4MRP GSH 7.89474
83 1VCO GLN 7.89474
84 3QX9 ATP 7.97101
85 3N7S 3N7 8.33333
86 1GVF PGH 8.55263
87 5ENZ UDP 8.55263
88 3RZ3 U94 9.21053
89 2Y69 CHD 9.27835
90 2UW1 GVM 9.86842
91 2GN2 C5P 9.86842
92 1ZGS XMM 9.86842
93 1TRD PGH 9.86842
94 5URY PAM 10.274
95 3TL1 JRO 10.5263
96 5NCB JZ3 10.5263
97 5Z84 CHD 10.5882
98 5ZCO CHD 10.5882
99 5W97 CHD 10.5882
100 3O01 DXC 11.1842
101 4WBD CIT 11.1842
102 2GBB CIT 11.1842
103 4RF7 ARG 11.1842
104 2YVE MBT 11.3514
105 5C1M CLR 11.8421
106 1PVC ILE SER GLU VAL 12.5
107 5M36 9SZ 12.5
108 6F5W KG1 12.5
109 1MJT ITU 13.1579
110 4JEM C5P 13.8158
111 2Q8M AMP 13.8158
112 5AJU RP5 14.4737
113 4HE2 AMP 14.4737
114 1W0H AMP 14.4737
115 2FJK 13P 14.4737
116 4BI7 PGA 15.1316
117 1ZED PNP 17.1053
118 2F64 12Q 17.7632
119 4XDA ADP 19.0789
120 4OGQ 2WD 19.7368
121 6H45 QEI 19.7368
122 1F8Y 5MD 39.4904
Pocket No.: 2; Query (leader) PDB : 4KXL; Ligand: 6C6; Similar sites found with APoc: 9
This union binding pocket(no: 2) in the query (biounit: 4kxl.bio2) has 49 residues
No: Leader PDB Ligand Sequence Similarity
1 2B99 RDL 1.97368
2 1R6N 434 3.94737
3 1VRP IOM 3.94737
4 5HWK BEZ 4.60526
5 4Z94 ATP 5.26316
6 3ITA AIC 7.23684
7 5FQ0 FLC 7.89474
8 2GWH PCI 9.21053
9 1XKD ICT 12.5
Pocket No.: 3; Query (leader) PDB : 4KXL; Ligand: 6C6; Similar sites found with APoc: 18
This union binding pocket(no: 3) in the query (biounit: 4kxl.bio1) has 52 residues
No: Leader PDB Ligand Sequence Similarity
1 2HPL ASP ASP LEU TYR GLY None
2 1XZ3 ICF None
3 3CTL S6P None
4 3M0J OAF 1.97368
5 1SQL GUN 2.05479
6 3AKI AH8 3.28947
7 1QDS PGA 3.94737
8 3MBI HSX 3.94737
9 4Z28 BTN 4.47761
10 2YP9 SIA CMO 5.26316
11 1C3X 8IG 5.26316
12 1LYX PGA 5.92105
13 4B9E FAH 5.92105
14 2JCB ADP 6.57895
15 5NGZ 2BG 6.59898
16 4BHL ARG 7.89474
17 1V1A ADP 9.21053
18 2O66 FLC 17.037
Pocket No.: 4; Query (leader) PDB : 4KXL; Ligand: 6C6; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 4kxl.bio1) has 52 residues
No: Leader PDB Ligand Sequence Similarity
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