Receptor
PDB id Resolution Class Description Source Keywords
3KU0 1.9 Å EC: 3.2.2.22 STRUCTURE OF GAP31 WITH ADENINE AT ITS BINDING POCKET GELONIUM MULTIFLORUM PLANT SEEDS GLYCOSIDASE DISULFIDE BOND GLYCOPROTEIN HYDROLASE PLANT DEFENSE PROTEIN SYNTHESIS INHIBITOR TOXIN
Ref.: A NEW ACTIVITY OF ANTI-HIV AND ANTI-TUMOR PROTEIN GAP31: DNA ADENOSINE GLYCOSIDASE--STRUCTURAL AND MODELING INSIGHT INTO ITS FUNCTIONS. BIOCHEM.BIOPHYS.RES.COMMUN. V. 391 340 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ADE A:800;
B:801;
Valid;
Valid;
none;
none;
submit data
135.127 C5 H5 N5 c1[nH...
NAG A:410;
B:411;
Part of Protein;
Part of Protein;
none;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3KU0 1.9 Å EC: 3.2.2.22 STRUCTURE OF GAP31 WITH ADENINE AT ITS BINDING POCKET GELONIUM MULTIFLORUM PLANT SEEDS GLYCOSIDASE DISULFIDE BOND GLYCOPROTEIN HYDROLASE PLANT DEFENSE PROTEIN SYNTHESIS INHIBITOR TOXIN
Ref.: A NEW ACTIVITY OF ANTI-HIV AND ANTI-TUMOR PROTEIN GAP31: DNA ADENOSINE GLYCOSIDASE--STRUCTURAL AND MODELING INSIGHT INTO ITS FUNCTIONS. BIOCHEM.BIOPHYS.RES.COMMUN. V. 391 340 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 13 families.
1 3KU0 - ADE C5 H5 N5 c1[nH]c2c(....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 3KU0 - ADE C5 H5 N5 c1[nH]c2c(....
50% Homology Family (47)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5DDZ - ASP ASP ASP MET GLY PHE GLY LEU PHE ASP n/a n/a
2 4MX5 ic50 = 28 uM 5MX C17 H17 N7 O4 c1ccc(cc1)....
3 4HV7 ic50 = 300 uM 19J C11 H11 N7 O5 c1c(nc2c(n....
4 3PX8 ic50 = 230 uM JP2 C7 H5 N5 O3 c1c(nc2c(n....
5 5GU4 Kd = 3.4 uM ASP ASP MET GLY PHE GLY LEU PHE ASP n/a n/a
6 1BR6 Ki = 0.6 mM PT1 C14 H12 N6 O3 c1cc(ccc1C....
7 4ESI ic50 = 70 uM 0RB C10 H9 N9 O2 c1c([nH]nn....
8 4HV3 ic50 = 115 uM 19L C21 H20 N8 O6 c1ccc2c(c1....
9 1BR5 Ki = 2 mM NEO C9 H11 N5 O4 c1c(nc2c(n....
10 3EJ5 ic50 = 0.27 mM EJ5 C14 H15 N3 O4 c1cc(ccc1C....
11 4MX1 ic50 = 209 uM 1MX C16 H16 N8 O3 c1ccc(cc1)....
12 3PX9 ic50 = 380 uM JP3 C12 H10 N6 O3 c1cc(oc1)C....
13 4HUO ic50 = 20 uM RS8 C18 H17 N7 O5 c1ccc(cc1)....
14 2P8N Kd = 700 uM ADE C5 H5 N5 c1[nH]c2c(....
15 1J1M - TRE C12 H22 O11 C([C@@H]1[....
16 4Q2V - 0XE C21 H18 O11 c1ccc(cc1)....
17 4HUP ic50 = 15 uM 19M C27 H26 N8 O6 c1ccc(cc1)....
18 1IFS - ADE C5 H5 N5 c1[nH]c2c(....
19 1IFU - FMC C10 H13 N5 O4 c1nc2c(c(n....
20 3HIO - C2X C51 H72 N21 O29 P5 CO[C@@H]1[....
21 2PJO Kd = 900 mM NMU C2 H6 N2 O CNC(=O)N
22 2R3D Kd = 1.4 M ACM C2 H5 N O CC(=O)N
23 3KU0 - ADE C5 H5 N5 c1[nH]c2c(....
24 2QET - ADE C5 H5 N5 c1[nH]c2c(....
25 1LPC - CMP C10 H12 N5 O6 P c1nc(c2c(n....
26 1GIU - ADE C5 H5 N5 c1[nH]c2c(....
27 1MRK - FMC C10 H13 N5 O4 c1nc2c(c(n....
28 1QD2 - ADE C5 H5 N5 c1[nH]c2c(....
29 1TCS - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
30 1MRJ - ADN C10 H13 N5 O4 c1nc(c2c(n....
31 1NLI Kd = 260 uM ADE C5 H5 N5 c1[nH]c2c(....
32 1GIS - DA C10 H14 N5 O6 P c1nc(c2c(n....
33 1AHB - FMP C10 H14 N5 O7 P c1nc2c(c(n....
34 1AHA - ADE C5 H5 N5 c1[nH]c2c(....
35 3N1N - GUN C5 H5 N5 O c1[nH]c2c(....
36 3V2K - ADE C5 H5 N5 c1[nH]c2c(....
37 3RL9 - ADE C5 H5 N5 c1[nH]c2c(....
38 3SJ6 - RIP C5 H10 O5 C1[C@H]([C....
39 1MRH - FMC C10 H13 N5 O4 c1nc2c(c(n....
40 3U6Z - ADE C5 H5 N5 c1[nH]c2c(....
41 1MRG - ADN C10 H13 N5 O4 c1nc(c2c(n....
42 1J1S - FMP C10 H14 N5 O7 P c1nc2c(c(n....
43 1D6A - GUN C5 H5 N5 O c1[nH]c2c(....
44 1QCI - ADE C5 H5 N5 c1[nH]c2c(....
45 3LE7 - ADE C5 H5 N5 c1[nH]c2c(....
46 3HIW Ki = 3.9 nM C2X C51 H72 N21 O29 P5 CO[C@@H]1[....
47 3HIV Ki = 7.5 nM TXN C37 H52 N15 O20 P3 CO[C@@H]1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ADE; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 ADE 1 1
2 PM6 0.5 0.742857
3 ES4 0.463415 0.685714
4 6AP 0.428571 0.9375
5 XQG 0.422222 0.648649
6 M02 0.411765 0.630435
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3KU0; Ligand: ADE; Similar sites found: 175
This union binding pocket(no: 1) in the query (biounit: 3ku0.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5MFI LYS ARG LYS ARG LYS ARG LYS ARG 0.02833 0.44106 None
2 5AEI LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 0.02672 0.42626 None
3 2ORV 4TA 0.0125 0.42555 None
4 3WUR O4B 0.006146 0.41387 None
5 1L6O SER LEU LYS LEU MET THR THR VAL 0.03842 0.40573 None
6 4WUJ FMN 0.02366 0.40505 None
7 2C3Q GTX 0.01623 0.4042 0.809717
8 5T2U NAP 0.03192 0.40961 1.20968
9 3FS1 MYR 0.01722 0.40725 1.30435
10 2Z6C FMN 0.02301 0.40252 1.55039
11 2FV5 541 0.02166 0.41573 1.59363
12 5BW4 SAM 0.02039 0.4106 1.59363
13 1BKC INN 0.002 0.44731 1.99203
14 1OKC CXT 0.01047 0.4302 1.99203
15 1N46 PFA 0.01588 0.42799 1.99203
16 2P1C GG3 0.02562 0.41981 1.99203
17 1M13 HYF 0.03439 0.4077 1.99203
18 1W4R TTP 0.01946 0.42279 2.05128
19 5FJN FAD 0.01593 0.44214 2.19298
20 5FJN BE2 0.01756 0.44214 2.19298
21 2EV1 OLA 0.01989 0.41158 2.25225
22 3LCV SAM 0.001951 0.47017 2.39044
23 4MOP 2H5 0.0213 0.44199 2.39044
24 1RYI FAD 0.02335 0.43349 2.39044
25 4HA6 FAD 0.02408 0.42641 2.39044
26 3KMZ EQO 0.01423 0.42468 2.39044
27 2YG3 FAD 0.03978 0.4163 2.39044
28 2LBD REA 0.02446 0.41114 2.39044
29 2DPM SAM 0.02444 0.40609 2.39044
30 4ITU NAI 0.04186 0.4042 2.39044
31 3O7B SAH 0.01855 0.40774 2.45902
32 3OVR 5SP 0.02071 0.41543 2.63158
33 2QJY SMA 0.03233 0.40204 2.6738
34 5ALC TIQ 0.02998 0.40776 2.77778
35 1N4W FAD 0.01042 0.45768 2.78884
36 1K0E TRP 0.004389 0.42691 2.78884
37 4E5N NAD 0.0223 0.42565 2.78884
38 5HGR 45D 0.02527 0.42203 2.78884
39 4MIX UD1 0.01423 0.40922 2.78884
40 1BRW URA 0.0105 0.40707 2.78884
41 1VQW FAD 0.04881 0.40242 2.78884
42 3RGA ILD 0.04402 0.40226 2.78884
43 4R38 RBF 0.01325 0.42588 2.85714
44 1YP1 LYS ASN LEU 0.01163 0.41185 2.9703
45 1HN4 MJI 0.01582 0.45602 3.05344
46 2Z6D FMN 0.02749 0.40137 3.07692
47 5JNN 6LM 0.0382 0.40286 3.15789
48 5DEY 59T 0.02702 0.43266 3.18725
49 3ICS FAD 0.02379 0.43071 3.18725
50 3ICR FAD 0.02617 0.42639 3.18725
51 4YDD MGD 0.03767 0.42569 3.18725
52 4YDD MD1 0.03767 0.42569 3.18725
53 3GDN FAD 0.04215 0.41698 3.18725
54 2C9E PID 0.01965 0.41669 3.18725
55 2GFD RDA 0.03362 0.40808 3.38983
56 2BVL UDP 0.01004 0.43565 3.58566
57 2BVL GLC 0.01004 0.43565 3.58566
58 4PJT 2YQ 0.0163 0.4261 3.58566
59 1IN4 ADP 0.0107 0.42295 3.58566
60 5UGH 8AJ 0.01336 0.41294 3.58566
61 3BOF HCS 0.008673 0.40901 3.58566
62 2FGE ALA ALA LEU THR ARG ALA 0.02402 0.40031 3.58566
63 5SVV FMN 0.01113 0.42872 3.64964
64 1OPK MYR 0.0002831 0.50251 3.98406
65 3E1T FAD 0.01251 0.45234 3.98406
66 3CGD COA 0.02313 0.45102 3.98406
67 3CGD FAD 0.02313 0.45102 3.98406
68 3CGD NAD 0.02313 0.45102 3.98406
69 3CGB FAD 0.009573 0.44848 3.98406
70 5BUK FAD 0.01836 0.44162 3.98406
71 4GCZ FMN 0.01288 0.42332 3.98406
72 5I39 FAD 0.03928 0.41533 3.98406
73 4JNA FAD 0.04386 0.41404 3.98406
74 5NTW 98N 0.03768 0.40617 3.98406
75 1V25 ANP 0.0463 0.40062 3.98406
76 1YDK GTX 0.02465 0.4145 4.05405
77 3HST MLR 0.021 0.40665 4.38247
78 5IXK 6EW 0.01336 0.43202 4.38596
79 2QX0 APC 0.0001921 0.50225 4.40252
80 2DBZ NAP 0.02537 0.41806 4.78088
81 3DWB RDF 0.02125 0.40438 4.78088
82 1Q3A NGH 0.01372 0.40025 4.84848
83 5CSD ACD 0.009621 0.44824 5.03145
84 1WG8 SAM 0.01124 0.42823 5.17928
85 5EY0 GTP 0.01441 0.40596 5.17928
86 1XIU REA 0.02549 0.40108 5.21739
87 1YP0 PEF 0.0138 0.42452 5.43933
88 1JNR FAD 0.02533 0.44151 5.57769
89 1H82 GZZ 0.02701 0.44048 5.57769
90 1H82 FAD 0.02398 0.44048 5.57769
91 1FL2 FAD 0.03111 0.41653 5.57769
92 4Q9M FPP 0.03719 0.40884 5.69106
93 4Q9M 2ZW 0.02055 0.40884 5.69106
94 4C9G CXT 0.01848 0.40784 5.9761
95 1EM6 NBG 0.03734 0.41658 6.13932
96 2OYS FMN 0.0212 0.41055 6.19835
97 3E8T UQ8 0.02491 0.43708 6.36364
98 1R27 MGD 0.009473 0.44142 6.3745
99 4USQ FAD 0.01845 0.43072 6.3745
100 4D79 ATP 0.01096 0.42284 6.3745
101 4RDI ATP 0.01908 0.40826 6.3745
102 4RDH AMP 0.01582 0.40508 6.3745
103 1JQ9 PHE LEU SER TYR LYS 0.00301 0.47321 6.61157
104 3FAL REA 0.01781 0.40941 6.61157
105 1RDT L79 0.02673 0.40592 6.61157
106 1V59 NAD 0.00802 0.42507 6.69456
107 1FFU FAD 0.02839 0.42032 6.74847
108 1REO FAD 0.0123 0.44637 6.77291
109 1NAA ABL 0.01831 0.44616 6.77291
110 1NAA 6FA 0.014 0.44616 6.77291
111 3UCL FAD 0.02431 0.44407 6.77291
112 3UCL NAP 0.02589 0.44407 6.77291
113 3UCL CYH 0.02431 0.44407 6.77291
114 5IR4 ZPE 0.04899 0.40814 6.77291
115 5ETR 5RW 0.000267 0.52972 6.8323
116 5ETR APC 0.000267 0.52972 6.8323
117 4M8E 29V 0.02424 0.40999 6.92641
118 4J7H TRH 0.02548 0.40289 7.17131
119 3KXC PLM 0.01218 0.42497 7.2165
120 5UWA 8ND 0.03217 0.41076 7.38916
121 1YOK P6L 0.02421 0.42227 7.56972
122 1YUC EPH 0.0278 0.41107 7.56972
123 1ZDU P3A 0.01303 0.42936 7.7551
124 5UNJ RJW 0.007373 0.42591 7.7551
125 4YSX FAD 0.03547 0.41513 7.96813
126 4IKR PVP 0.02669 0.40102 7.96813
127 1D4D FAD 0.01301 0.45056 8.36653
128 5IGI GMP 0.04496 0.40815 8.36653
129 5IGI ZIT 0.04666 0.40815 8.36653
130 3ZS7 ATP 0.02303 0.40233 8.36653
131 2Y31 SMQ 0.04536 0.40054 8.36653
132 1ATL 0QI 0.01417 0.42033 8.41584
133 2Z3Y F2N 0.02042 0.43556 8.76494
134 5IH1 GDP 0.03267 0.42867 8.76494
135 5IH1 6BQ 0.03267 0.42867 8.76494
136 4EIP FAD 0.04468 0.41823 8.76494
137 3EM1 TYD 0.01576 0.4044 8.90411
138 3CTY FAD 0.007071 0.46837 9.16335
139 2BRY FAD 0.03926 0.41036 9.56175
140 3LZW NAP 0.009504 0.46668 9.96016
141 3LZW FAD 0.005318 0.46668 9.96016
142 4QJR PIZ 0.0367 0.40286 10.2041
143 3QXV MTX 0.01668 0.41538 10.3175
144 3KLJ FAD 0.01458 0.43599 10.3586
145 2DKH FAD 0.01405 0.43544 10.3586
146 2VVM FAD 0.02388 0.42256 10.3586
147 1ZDT PEF 0.01872 0.42228 10.3734
148 5TTJ FAD 0.008892 0.451 11.1554
149 5EFW FMN 0.01443 0.42047 11.7241
150 1KRP DT DT PST 0.02312 0.41593 11.9522
151 2VL8 CTS 0.01707 0.41013 11.9522
152 2VL8 UDP 0.0147 0.41013 11.9522
153 3AD8 FAD 0.02795 0.44604 12.1212
154 3AD8 PYC 0.02795 0.44604 12.1212
155 1I1Q TRP 0.009737 0.41072 12.3506
156 3VRV YSD 0.04999 0.41794 12.749
157 2YVJ NAI 0.01579 0.41274 12.844
158 1R6U TYM 0.02867 0.40876 13.1474
159 2D5Z L35 0.04131 0.43067 13.4752
160 4IVG ANP 0.02185 0.413 13.5458
161 4C2V YJA 0.03206 0.41318 13.6364
162 4EES FMN 0.01502 0.42103 14.7826
163 4II2 ATP 0.005993 0.43916 15.3374
164 2VVL FAD 0.03654 0.41181 15.9363
165 3OJI PYV 0.02902 0.40582 16.9312
166 5G3N X28 0.004281 0.45156 17.3228
167 2ZFZ ARG 0.03787 0.41355 18.9873
168 2GAG FOA 0.009102 0.46253 22.2222
169 2GAG FAD 0.009102 0.46253 22.2222
170 2GAG NAD 0.02296 0.42933 22.2222
171 4F07 FAD 0.01808 0.40692 23.1579
172 1TMM HHR 0.0005851 0.50001 24.6835
173 1TMM APC 0.0006231 0.50001 24.6835
174 1M48 FRG 0.006608 0.41976 30.0752
175 5DJT FMN 0.01202 0.42519 31.1475
Pocket No.: 2; Query (leader) PDB : 3KU0; Ligand: ADE; Similar sites found: 32
This union binding pocket(no: 2) in the query (biounit: 3ku0.bio2) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2GTE VA 0.01182 0.42455 None
2 2GJ3 FAD 0.01897 0.40632 None
3 3FJO FMN 0.02315 0.40476 2.39044
4 4I4B 1CV 0.04001 0.40564 2.78884
5 3DHV DAL AMP 0.03056 0.40486 3.18725
6 3P0K FAD 0.03319 0.40408 3.18725
7 4NNB OAA 0.04873 0.40206 3.58566
8 1C9K 5GP 0.01561 0.40486 3.88889
9 1QAN SAH 0.01885 0.41453 4.09836
10 2FP2 TSA 0.02695 0.40292 4.21687
11 1ID0 ANP 0.02045 0.40086 4.60526
12 5TQZ GLC 0.006825 0.40794 4.66667
13 1B8U NAD 0.02808 0.40417 4.78088
14 1YSL COA 0.03149 0.40134 5.17928
15 3PVT 3HC 0.04473 0.43481 5.57769
16 1P9P SAH 0.01868 0.4123 5.9761
17 5X62 SAH 0.02301 0.40456 5.9761
18 3GD4 FAD 0.03977 0.41505 6.3745
19 1XKD NAP 0.03312 0.40824 6.3745
20 1FM9 9CR 0.02128 0.41039 6.72269
21 5K52 OCD 0.01841 0.40798 6.77291
22 4D7E FAD 0.04756 0.40696 7.17131
23 1ZGA HMK 0.01798 0.40087 7.56972
24 3JQM GTP 0.02115 0.40252 7.64331
25 1RSG FAD 0.04177 0.41288 7.96813
26 4W6Z 8ID 0.03951 0.41054 7.96813
27 4J36 FAD 0.02613 0.41904 9.16335
28 1OBV FMN 0.02481 0.40141 9.46746
29 2DKH 3HB 0.02454 0.42574 10.3586
30 3G08 FEE 0.04501 0.41959 11.1111
31 3AD8 NAD 0.01837 0.43089 12.1212
32 3L9R L9R 0.04803 0.40554 12.2449
Feedback