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Receptor
PDB id Resolution Class Description Source Keywords
4KXM 2.24 Å EC: 3.2.2.- CRYSTAL STRUCTURE OF DNPH1 (RCL) WITH N6-ISOPENTENYL-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
6IA C:201;
B:201;
D:201;
A:201;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 Ki = 3.3 uM
417.354 C15 H24 N5 O7 P CC(C)...
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: 6IA; Similar ligands found: 145
No: Ligand ECFP6 Tc MDL keys Tc
1 6IA 1 1
2 6K6 0.666667 0.896104
3 6C6 0.643678 0.875
4 2SA 0.622222 0.851852
5 AMP 0.578313 0.858974
6 A 0.578313 0.858974
7 IMO 0.55814 0.822785
8 6MD 0.518519 0.759494
9 PGS 0.51087 0.767442
10 ABM 0.505618 0.860759
11 ADP 0.48913 0.8375
12 A2D 0.488889 0.814815
13 PRX 0.484211 0.8625
14 5AL 0.479592 0.82716
15 M33 0.478723 0.82716
16 ITT 0.478723 0.8125
17 AU1 0.478723 0.817073
18 A12 0.478261 0.829268
19 71V 0.478261 0.788235
20 BA3 0.478261 0.814815
21 AP2 0.478261 0.829268
22 7RP 0.477778 0.844156
23 HEJ 0.473684 0.8375
24 50T 0.473684 0.82716
25 ATP 0.473684 0.8375
26 B4P 0.473118 0.814815
27 AP5 0.473118 0.814815
28 9ZD 0.470588 0.831325
29 25A 0.470588 0.8375
30 9ZA 0.470588 0.831325
31 AQP 0.46875 0.8375
32 APC 0.46875 0.829268
33 5FA 0.46875 0.8375
34 AN2 0.468085 0.82716
35 AT4 0.468085 0.807229
36 SRA 0.466667 0.817073
37 AIR 0.464286 0.797468
38 ADX 0.463158 0.741573
39 CA0 0.463158 0.795181
40 AHX 0.461538 0.821429
41 N6P 0.461538 0.833333
42 XAH 0.458716 0.835294
43 ACP 0.458333 0.839506
44 5SV 0.456311 0.843373
45 8QN 0.456311 0.82716
46 AMZ 0.454545 0.768293
47 ANP 0.454545 0.817073
48 TAT 0.454545 0.807229
49 T99 0.454545 0.807229
50 ACQ 0.454545 0.839506
51 AR6 0.453608 0.814815
52 APR 0.453608 0.814815
53 4AD 0.451923 0.819277
54 SAP 0.44898 0.797619
55 AGS 0.44898 0.797619
56 ADV 0.44898 0.807229
57 AD9 0.44898 0.817073
58 RBY 0.44898 0.807229
59 TXA 0.448598 0.807229
60 PTJ 0.448598 0.865854
61 ARU 0.447619 0.833333
62 YLP 0.447368 0.837209
63 DAL AMP 0.446602 0.804878
64 NIA 0.444444 0.715909
65 6YZ 0.441176 0.839506
66 SRP 0.441176 0.851852
67 AAM 0.44086 0.858974
68 RMB 0.44086 0.818182
69 LAD 0.439252 0.855422
70 C2R 0.438202 0.759036
71 AMO 0.438095 0.829268
72 PAJ 0.438095 0.855422
73 TT8 0.436893 0.72619
74 YLB 0.435897 0.858824
75 1ZZ 0.435185 0.813953
76 ME8 0.435185 0.857143
77 FYA 0.435185 0.85
78 NB8 0.435185 0.8
79 RBZ 0.434783 0.820513
80 ADP PO3 0.434343 0.8125
81 ARG AMP 0.433628 0.825581
82 A22 0.432692 0.82716
83 MAP 0.432692 0.797619
84 ATF 0.431373 0.807229
85 5AS 0.427083 0.73913
86 WAQ 0.425926 0.809524
87 GAP 0.425743 0.817073
88 JLN 0.425532 0.768293
89 FAI 0.425532 0.768293
90 P2P 0.425532 0.822785
91 7RA 0.425532 0.848101
92 ADQ 0.424528 0.817073
93 A1R 0.424528 0.853659
94 LMS 0.423913 0.722222
95 1RB 0.423913 0.805195
96 YLC 0.423729 0.857143
97 3US 0.422764 0.793103
98 SON 0.42268 0.829268
99 48N 0.422414 0.8
100 AYB 0.421488 0.848837
101 7MD 0.421053 0.835294
102 DLL 0.420561 0.804878
103 TSB 0.419048 0.717391
104 MTP 0.418605 0.690476
105 MYR AMP 0.418182 0.793103
106 A5A 0.417476 0.725275
107 ADP ALF 0.417476 0.755814
108 ALF ADP 0.417476 0.755814
109 IOT 0.416667 0.827586
110 OAD 0.416667 0.817073
111 PMO 0.416667 0.797468
112 9X8 0.416667 0.797619
113 LEU LMS 0.416667 0.771739
114 OOB 0.415094 0.804878
115 VO4 ADP 0.413462 0.804878
116 ADP VO4 0.413462 0.804878
117 AP0 0.411765 0.8
118 7MC 0.411765 0.837209
119 A3R 0.411215 0.853659
120 LSS 0.411215 0.78022
121 B5M 0.410714 0.797619
122 VMS 0.409524 0.747253
123 54H 0.409524 0.747253
124 52H 0.409524 0.73913
125 3OD 0.409091 0.817073
126 BIS 0.409091 0.809524
127 1PR 0.409091 0.776471
128 GA7 0.408696 0.875
129 NVA LMS 0.407407 0.752688
130 00A 0.407407 0.767442
131 36A 0.40678 0.704545
132 F2R 0.406504 0.837209
133 25L 0.405405 0.82716
134 5GP 0.40404 0.785714
135 G 0.40404 0.785714
136 ADP BMA 0.40367 0.795181
137 3UK 0.40367 0.795181
138 3DH 0.402174 0.728395
139 A3P 0.402062 0.835443
140 A2P 0.402062 0.822785
141 9SN 0.401786 0.758621
142 YLA 0.401639 0.816092
143 A A 0.4 0.8375
144 PR8 0.4 0.845238
145 B5V 0.4 0.785714
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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