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Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
6C6 D:201;
C:201;
B:201;
A:201;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Ki = 1.2 uM
415.338 C15 H22 N5 O7 P c1nc(...
SO4 D:202;
C:202;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
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: 6C6; Similar ligands found: 124
No: Ligand ECFP6 Tc MDL keys Tc
1 6C6 1 1
2 6IA 0.643678 0.875
3 2SA 0.611111 0.896104
4 A 0.585366 0.905405
5 AMP 0.585366 0.905405
6 6K6 0.585106 0.893333
7 IMO 0.564706 0.866667
8 AP2 0.5 0.896104
9 ITT 0.5 0.855263
10 PGS 0.5 0.804878
11 BA3 0.5 0.857143
12 A12 0.5 0.896104
13 ATP 0.494624 0.881579
14 HEJ 0.494624 0.881579
15 ADP 0.494505 0.881579
16 AP5 0.494505 0.857143
17 B4P 0.494505 0.857143
18 A2D 0.494382 0.857143
19 ABM 0.494382 0.857143
20 25A 0.49 0.881579
21 5FA 0.489362 0.881579
22 AQP 0.489362 0.881579
23 AT4 0.48913 0.848101
24 6MD 0.487805 0.753247
25 AU1 0.483871 0.858974
26 71V 0.483516 0.82716
27 T99 0.474227 0.848101
28 TAT 0.474227 0.848101
29 APC 0.473684 0.896104
30 AN2 0.473118 0.87013
31 SRA 0.47191 0.858974
32 AGS 0.46875 0.8375
33 SAP 0.46875 0.8375
34 CA0 0.468085 0.835443
35 ADX 0.468085 0.776471
36 M33 0.468085 0.846154
37 N6P 0.466019 0.878378
38 ACP 0.463158 0.883117
39 50T 0.463158 0.87013
40 6YZ 0.46 0.883117
41 AMZ 0.45977 0.807692
42 ACQ 0.459184 0.883117
43 ANP 0.459184 0.858974
44 PRX 0.458333 0.883117
45 AR6 0.458333 0.857143
46 APR 0.458333 0.857143
47 PR8 0.457143 0.911392
48 ADV 0.453608 0.871795
49 RBY 0.453608 0.871795
50 ADP PO3 0.453608 0.855263
51 AD9 0.453608 0.858974
52 AIR 0.452381 0.84
53 7RP 0.450549 0.890411
54 ATF 0.45 0.848101
55 JLN 0.445652 0.807692
56 P2P 0.445652 0.866667
57 1RB 0.444444 0.849315
58 C2R 0.443182 0.797468
59 5AL 0.44 0.846154
60 RBZ 0.43956 0.815789
61 ARU 0.438095 0.785714
62 AHX 0.438095 0.839506
63 MAP 0.436893 0.8375
64 A22 0.436893 0.87013
65 ADP ALF 0.435644 0.792683
66 ALF ADP 0.435644 0.792683
67 25L 0.435185 0.87013
68 NIA 0.433333 0.75
69 9ZD 0.432692 0.82716
70 9ZA 0.432692 0.82716
71 8QN 0.432692 0.846154
72 ADP VO4 0.431373 0.846154
73 VO4 ADP 0.431373 0.846154
74 SRP 0.431373 0.871795
75 AAM 0.430108 0.905405
76 RMB 0.430108 0.837838
77 FAI 0.430108 0.807692
78 7RA 0.430108 0.893333
79 GAP 0.43 0.8125
80 A3R 0.428571 0.897436
81 4AD 0.428571 0.860759
82 ADQ 0.428571 0.835443
83 AMO 0.428571 0.871795
84 A1R 0.428571 0.897436
85 SON 0.427083 0.896104
86 PTJ 0.425926 0.817073
87 FYA 0.425926 0.92
88 NB8 0.425926 0.839506
89 DLL 0.424528 0.846154
90 ADP BMA 0.420561 0.8125
91 OOB 0.419048 0.846154
92 5SV 0.419048 0.886076
93 PAJ 0.415094 0.785714
94 LMS 0.413043 0.755814
95 TXA 0.412844 0.825
96 BIS 0.412844 0.873418
97 3OD 0.412844 0.835443
98 7MD 0.412281 0.876543
99 00A 0.411215 0.804878
100 XAH 0.410714 0.876543
101 DAL AMP 0.409524 0.822785
102 5GP 0.408163 0.825
103 G 0.408163 0.825
104 9X8 0.407407 0.814815
105 3UK 0.407407 0.835443
106 OAD 0.407407 0.835443
107 A2P 0.40625 0.866667
108 PMO 0.40625 0.815789
109 A3P 0.40625 0.88
110 HFD 0.405941 0.8375
111 WAQ 0.40367 0.922078
112 B5V 0.40367 0.825
113 A A 0.40367 0.881579
114 P5A 0.40367 0.797753
115 LAD 0.40367 0.898734
116 IMP 0.402062 0.846154
117 5AS 0.402062 0.733333
118 RGT 0.401786 0.848101
119 ATP A A A 0.401786 0.844156
120 YAP 0.401786 0.860759
121 FA5 0.401786 0.871795
122 AFH 0.4 0.807229
123 1ZZ 0.4 0.853659
124 ME8 0.4 0.831325
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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