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Receptor
PDB id Resolution Class Description Source Keywords
4P5E 1.35 Å EC: 3.2.2.- CRYSTAL STRUCTURE OF HUMAN DNPH1 (RCL) WITH 6-NAPHTHYL-PURIN RIBOSIDE-MONOPHOSPHATE HOMO SAPIENS RCL DNPH1 INHIBITOR ROSSMANN FOLD HYDROLASE
Ref.: 6-(HETERO)ARYLPURINE NUCLEOTIDES AS INHIBITORS OF T ONCOGENIC TARGET DNPH1: SYNTHESIS, STRUCTURAL STUDI CYTOTOXIC ACTIVITIES. EUR.J.MED.CHEM. V. 85C 418 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
N6P A:201;
B:201;
Valid;
Valid;
none;
none;
Ki = 2.8 uM
458.361 C20 H19 N4 O7 P c1ccc...
CA B:202;
Part of Protein;
none;
submit data
40.078 Ca [Ca+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4P5E 1.35 Å EC: 3.2.2.- CRYSTAL STRUCTURE OF HUMAN DNPH1 (RCL) WITH 6-NAPHTHYL-PURIN RIBOSIDE-MONOPHOSPHATE HOMO SAPIENS RCL DNPH1 INHIBITOR ROSSMANN FOLD HYDROLASE
Ref.: 6-(HETERO)ARYLPURINE NUCLEOTIDES AS INHIBITORS OF T ONCOGENIC TARGET DNPH1: SYNTHESIS, STRUCTURAL STUDI CYTOTOXIC ACTIVITIES. EUR.J.MED.CHEM. V. 85C 418 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 4P5E Ki = 2.8 uM N6P C20 H19 N4 O7 P c1ccc2cc(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: N6P; Similar ligands found: 84
No: Ligand ECFP6 Tc MDL keys Tc
1 N6P 1 1
2 A 0.527473 0.942029
3 AMP 0.527473 0.942029
4 IMO 0.526882 0.955882
5 ITT 0.5 0.942029
6 HEJ 0.48 0.915493
7 ATP 0.48 0.915493
8 ADP 0.479592 0.915493
9 6K6 0.476636 0.928571
10 5FA 0.475248 0.915493
11 AQP 0.475248 0.915493
12 PGS 0.47 0.855263
13 71V 0.469388 0.855263
14 2SA 0.466667 0.878378
15 6C6 0.466019 0.878378
16 B4P 0.464646 0.915493
17 AP5 0.464646 0.915493
18 A2D 0.463918 0.915493
19 25A 0.462963 0.942857
20 6IA 0.461538 0.833333
21 AT4 0.46 0.878378
22 BA3 0.454545 0.915493
23 ABM 0.44898 0.888889
24 6YZ 0.448598 0.890411
25 TAT 0.447619 0.878378
26 T99 0.447619 0.878378
27 ACQ 0.447619 0.890411
28 APC 0.446602 0.878378
29 AN2 0.445545 0.902778
30 CA0 0.441176 0.864865
31 ADX 0.441176 0.8
32 M33 0.441176 0.876712
33 A12 0.44 0.878378
34 AP2 0.44 0.878378
35 3UK 0.4375 0.890411
36 50T 0.436893 0.902778
37 ACP 0.436893 0.890411
38 OOB 0.436364 0.902778
39 RMB 0.434343 0.925373
40 ANP 0.433962 0.890411
41 B5V 0.433628 0.878378
42 1RB 0.43299 0.939394
43 PRX 0.432692 0.864865
44 APR 0.432692 0.888889
45 AR6 0.432692 0.888889
46 5AL 0.429907 0.876712
47 DLL 0.428571 0.902778
48 SRA 0.428571 0.890411
49 AGS 0.428571 0.866667
50 AD9 0.428571 0.890411
51 SAP 0.428571 0.866667
52 A22 0.427273 0.929577
53 AU1 0.427184 0.890411
54 25L 0.426087 0.929577
55 ATF 0.425926 0.878378
56 ADQ 0.419643 0.890411
57 B5M 0.418803 0.866667
58 RGT 0.418803 0.878378
59 FYA 0.417391 0.902778
60 ARU 0.415929 0.833333
61 RBY 0.415094 0.853333
62 ADV 0.415094 0.853333
63 HFD 0.411215 0.866667
64 8QN 0.410714 0.876712
65 7RP 0.41 0.984848
66 SRP 0.409091 0.853333
67 PR8 0.408696 0.8
68 AIR 0.408602 0.871429
69 V3L 0.407407 0.915493
70 PAJ 0.40708 0.810127
71 A1R 0.40708 0.831169
72 FA5 0.40678 0.878378
73 PTJ 0.405172 0.844156
74 6AD 0.40367 0.833333
75 00A 0.403509 0.855263
76 6V0 0.403226 0.844156
77 C2R 0.402062 0.824324
78 AMZ 0.402062 0.835616
79 ADP PO3 0.401869 0.887324
80 MAP 0.401786 0.866667
81 G 0.4 0.853333
82 RBZ 0.4 0.898551
83 4UV 0.4 0.866667
84 5GP 0.4 0.853333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4P5E; Ligand: N6P; Similar sites found with APoc: 118
This union binding pocket(no: 1) in the query (biounit: 4p5e.bio2) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 2CHT TSA None
2 2CYB TYR None
3 3BBD SAH None
4 4NTO 1PW 1.31579
5 5TED SKM 1.31579
6 3KC1 2T6 1.31579
7 2RIO ADP 1.31579
8 3EXS 5RP 1.31579
9 4JLS 3ZE 1.97368
10 2Q37 3AL 1.97368
11 3O7J 2AL 1.97368
12 3E3U NVC 1.97368
13 1C3X 8IG 1.97368
14 5YSI NCA 1.97368
15 4E28 9MZ 1.97368
16 3B6O TMP 1.97368
17 2BVE PH5 2.52101
18 4MZU TDR 2.63158
19 5NGZ 2BG 2.63158
20 4JOB TLA 2.63158
21 6E1Q CFA 2.63158
22 3TY3 GGG 2.63158
23 5TQZ GLC 2.66667
24 5DQY BEZ 2.85714
25 4WBD CIT 3.28947
26 3SBZ MLI 3.28947
27 3MBI HSX 3.28947
28 3R75 PYR 3.28947
29 1QDS PGA 3.28947
30 3R7F CP 3.28947
31 2X1E X1E 3.28947
32 3Q9T FAY 3.63951
33 1WLJ U5P 3.94737
34 4AF5 CIT 3.94737
35 2YPI PGA 3.94737
36 2ZE3 AKG 3.94737
37 3HQP OXL 3.94737
38 1WPQ 13P 3.94737
39 3UEC ALA ARG TPO LYS 3.94737
40 4XMF HSM 3.94737
41 2JLD AG1 3.94737
42 2EUG URA 3.94737
43 6F97 FAD 3.94737
44 1JNR FAD 3.94737
45 3QH2 3NM 4.60526
46 1CT9 GLN 4.60526
47 1GVF PGH 4.60526
48 5J3Z 6FQ 4.60526
49 1SW0 PGA 4.60526
50 5GZ9 MAN 4.60526
51 5F7U GLC GLC 4.60526
52 3AB4 THR 4.75059
53 5YJS SAL 5.26316
54 1O5Q PYR 5.26316
55 5CIC 51R 5.26316
56 5LXT GTP 5.26316
57 4CP8 MLI 5.26316
58 4G86 BNT 5.92105
59 3E7S AT2 5.92105
60 4NOS ITU 5.92105
61 2R5N RP5 5.92105
62 2R5N TPP 5.92105
63 4RYV ZEA 5.92105
64 6H3O FAD 5.92105
65 1TZJ A3B 5.92105
66 5LX6 78P 6.57895
67 2C6Q NDP 6.57895
68 4XDA RIB 6.57895
69 4E3Q PMP 6.57895
70 3B6C SDN 6.57895
71 4GYS MLI 7.23684
72 5HSA FAS 7.23684
73 1J71 THR ILE THR SER 7.89474
74 4M0R 644 7.89474
75 5HWK BEZ 8.55263
76 4JB1 NAP 8.55263
77 1GTE IUR 8.55263
78 1GTE FMN 8.55263
79 1MJT ITU 8.93372
80 2P3V SRT 9.21053
81 4OB6 S2T 9.21053
82 1TL2 NDG 9.21053
83 5W6Y TRP 9.86842
84 1RM6 PCD 9.86842
85 1TKB N1T 9.86842
86 5URY PAM 10.274
87 3QVP FAD 11.1842
88 4YSX MLI 11.1842
89 4K7O EKZ 11.1842
90 1PVC ILE SER GLU VAL 11.7647
91 1T36 ORN 11.8421
92 4WZA ADP 12.5
93 4WZA ACP 12.5
94 2GMH FAD 12.5
95 5JCM FAD 13.1579
96 5JCM NAD 13.1579
97 5JCM ISD 13.1579
98 5AJU RP5 13.8158
99 1C9K 5GP 13.8158
100 2MBR EPU 14.4737
101 5L2R MLA 15.1316
102 1S2D ADE 15.5689
103 1RP0 AHZ 15.7895
104 2JCB ADP 15.7895
105 5VKM GAL SIA 17.1053
106 2MJP ANP 17.7632
107 6B4H IHP 18.4211
108 3OBT SLB 19.0789
109 6H45 QEI 19.0789
110 4HE2 AMP 19.7368
111 5FS0 5JC 20.3947
112 5FPE 3TR 20.3947
113 1F8Y 5MD 22.3684
114 4OHB 5HM 23.0263
115 2EB5 OXL 23.0263
116 4JEM C5P 23.6842
117 5YRM BGC GLC 26.0563
118 5YRJ BGC GLC 26.7606
Pocket No.: 2; Query (leader) PDB : 4P5E; Ligand: N6P; Similar sites found with APoc: 94
This union binding pocket(no: 2) in the query (biounit: 4p5e.bio2) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 2GBB CIT None
2 1WUW TSU None
3 1L7N ALF None
4 1W0H AMP None
5 3C3N FMN None
6 3OII SAH None
7 3S6X SIA GAL BGC 1.31579
8 5XLA SIA 1.97368
9 2IID FAD 1.97368
10 2IID PHE 1.97368
11 1REO FAD 1.97368
12 2UUU FAD 2.63158
13 2UUU PL3 2.63158
14 2BDG PBZ 2.63158
15 5CXX FER 2.63158
16 3TAO PGH 2.99625
17 4JEJ 1GP 3.28947
18 2Q8M AMP 3.28947
19 1SBR VIB 3.28947
20 3N9R TD3 3.28947
21 4RKX 3S9 3.44828
22 2PIE GLU LEU LYS TPO GLU ARG TYR 3.62319
23 2Z3Y F2N 3.94737
24 1I7Q BEZ 3.94737
25 2ZL4 ALA ALA ALA ALA 3.94737
26 1WD4 AHR 3.94737
27 3HQP FDP 3.94737
28 5C9J DAO 4.0404
29 1E6E FAD 4.60526
30 2PNC CLU 4.60526
31 1Q9I TEO 4.60526
32 1Q9I FAD 4.60526
33 3AYI FAD 4.60526
34 3AYI HCI 4.60526
35 1G0N PHH 4.60526
36 1G0N NDP 4.60526
37 5XFV FMN 4.60526
38 5W3X ACO 4.60526
39 1BO4 COA 4.60526
40 2BW7 APC 5.02283
41 2YP9 SIA CMO 5.26316
42 1ZPD DPX 5.26316
43 4BG4 ARG 5.26316
44 1VKF CIT 5.26316
45 1BZL FAD 5.26316
46 2BTM PGA 5.26316
47 4IV9 FAD 5.26316
48 4J7U YTZ 5.26316
49 4J7U NAP 5.26316
50 3HGM ATP 5.44218
51 4ITU 1HS 5.57621
52 4D9C PMP 5.92105
53 2JGV ADP 5.92105
54 2ZRU FMN 5.92105
55 2C6Q IMP 6.57895
56 3ZEI AWH 6.57895
57 5AE2 FAD 6.57895
58 5AE2 FYC 6.57895
59 4FHT DHB 6.57895
60 2Z9I GLY ALA THR VAL 6.57895
61 1D6S PLP MET 6.57895
62 5H6S HDH 6.57895
63 1D6S MET PLP 6.57895
64 4ZUL UN1 7.23684
65 4RLQ 3SK 7.23684
66 2Z6I FMN 7.23684
67 3CTL S6P 7.23684
68 3NYC FAD 7.23684
69 3NYC IAR 7.23684
70 5K0A FAD 7.23684
71 5NCB JZ3 7.89474
72 5OSW DIU 7.89474
73 2VBF TPP 8.55263
74 1QO8 FAD 8.55263
75 3FPZ AHZ 8.55263
76 2FJK 13P 8.55263
77 5MBX SP5 9.21053
78 5MBX FAD 9.21053
79 4YNU LGC 9.86842
80 3RNM FAD 9.86842
81 2F5Z FAD 9.86842
82 1GPJ CIT 11.1842
83 5ODQ FAD 11.8421
84 1J0D 5PA 11.8421
85 1YY5 FAD 12.5
86 1RJW ETF 13.1579
87 5KGS 6SR 14.4737
88 4RF7 ARG 14.4737
89 1W6P NDG GAL 17.9104
90 3A75 GLU 18.4211
91 5YRL GLC GLC 26.0563
92 5YRF GLC GLC 26.7606
93 5YRG BGC GLC 26.7606
94 2PHX MAN MAN MAN MAN 28.9474
Pocket No.: 3; Query (leader) PDB : 4P5E; Ligand: N6P; Similar sites found with APoc: 8
This union binding pocket(no: 3) in the query (biounit: 4p5e.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 5WBF LAC 1.97368
2 5ZYN SIN 4.60526
3 3ITA AIC 6.57895
4 2ZX2 RAM 6.57895
5 4JB1 FAD 8.55263
6 1EYQ NAR 8.55263
7 2ITM XUL 12.5
8 3KIH GDL 14.433
Pocket No.: 4; Query (leader) PDB : 4P5E; Ligand: N6P; Similar sites found with APoc: 24
This union binding pocket(no: 4) in the query (biounit: 4p5e.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 1TE2 PGA 1.31579
2 3QFA FAD 2.58621
3 2WGV CIT 2.63158
4 1WOG 16D 2.63158
5 5ZBC FAD 3.28947
6 2BLE 5GP 4.08719
7 5VLQ ANP 5.26316
8 5LA1 XYP 5.26316
9 2A8X FAD 5.26316
10 5U8U FAD 5.26316
11 2Z6J FMN 5.26316
12 1PVN MZP 5.26316
13 4FXQ G9L 6.57895
14 4FFG 0U8 6.57895
15 1H82 GZZ 8.55263
16 1H82 FAD 8.55263
17 5J5Z FAD 9.86842
18 4FC7 NAP 10.5263
19 4FC7 COA 10.5263
20 3LAD FAD 12.5
21 4YRY NAD 13.8158
22 4YRY FAD 13.8158
23 5N0J FAD 17.1053
24 5HX1 UMP 19.5652
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