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Receptor
PDB id Resolution Class Description Source Keywords
4GNC 1.75 Å EC: 3.1.1.17 HUMAN SMP30/GNL-1,5-AG COMPLEX HOMO SAPIENS BETA PROPELLER STRUCTURE HYDROLASE
Ref.: STRUCTURAL BASIS OF THE GAMMA-LACTONE-RING FORMATIO ASCORBIC ACID BIOSYNTHESIS BY THE SENESCENCE MARKER PROTEIN-30/GLUCONOLACTONASE PLOS ONE V. 8 53706 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ASO A:302;
A:303;
B:302;
B:304;
B:303;
Invalid;
Valid;
Valid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
164.156 C6 H12 O5 C1[C@...
CA A:301;
B:301;
Part of Protein;
Part of Protein;
none;
none;
submit data
40.078 Ca [Ca+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4GNC 1.75 Å EC: 3.1.1.17 HUMAN SMP30/GNL-1,5-AG COMPLEX HOMO SAPIENS BETA PROPELLER STRUCTURE HYDROLASE
Ref.: STRUCTURAL BASIS OF THE GAMMA-LACTONE-RING FORMATIO ASCORBIC ACID BIOSYNTHESIS BY THE SENESCENCE MARKER PROTEIN-30/GLUCONOLACTONASE PLOS ONE V. 8 53706 2013
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4GNC - ASO C6 H12 O5 C1[C@@H]([....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4GNC - ASO C6 H12 O5 C1[C@@H]([....
2 4GN8 - ASO C6 H12 O5 C1[C@@H]([....
3 4GNA - XYL C5 H12 O5 C([C@@H](C....
4 4GN9 - BGC C6 H12 O6 C([C@@H]1[....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4GNC - ASO C6 H12 O5 C1[C@@H]([....
2 4GN8 - ASO C6 H12 O5 C1[C@@H]([....
3 4GNA - XYL C5 H12 O5 C([C@@H](C....
4 4GN9 - BGC C6 H12 O6 C([C@@H]1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ASO; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 ASO 1 1
2 R1X 0.692308 0.848485
3 32O 0.4 0.757576
4 RIB 0.4 0.757576
5 Z6J 0.4 0.757576
6 FUB 0.4 0.757576
7 AHR 0.4 0.757576
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4GNC; Ligand: ASO; Similar sites found with APoc: 125
This union binding pocket(no: 1) in the query (biounit: 4gnc.bio2) has 8 residues
No: Leader PDB Ligand Sequence Similarity
1 2ABS ACP 1.00334
2 1Z8O DEB 1.33779
3 3MA0 XYP 1.33779
4 3DAK ANP 1.37931
5 1DMH LIO 1.67224
6 5LNQ CAA 1.67224
7 2A1L PCW 1.85185
8 4HKP TKW 2.00669
9 4XDZ NDP 2.00669
10 4G5G GDP 2.00669
11 1KIJ NOV 2.00669
12 1B7H LYS NLE LYS 2.00669
13 3U6B GDP 2.00669
14 2A9G ARG 2.00669
15 2QCD U5P 2.30769
16 4BR5 ANP 2.34114
17 1P7L ANP 2.34114
18 1P7L MET 2.34114
19 1P7L PPK 2.34114
20 1P7L SAM 2.34114
21 4XRZ SI6 2.34114
22 3BXF FBP 2.35294
23 1TMX HGX 2.38908
24 6GI2 8SW 2.48227
25 1OPK P16 2.67559
26 4RJK TPP 2.67559
27 4ZVI 4S4 2.67559
28 5W75 GDP 2.67559
29 5UGH 8AJ 2.67559
30 3FV1 DYH 2.73438
31 1UKZ AMP 2.95567
32 1UKZ ADP 2.95567
33 4MDH NAD 3.01003
34 4K33 ACP 3.01003
35 4AUA 4AU 3.01003
36 2B9J ADP 3.01003
37 2B9F ADP 3.01003
38 1RQ5 CTT 3.34448
39 3SSO SAH 3.34448
40 1ADO 13P 3.34448
41 1NAA 6FA 3.34448
42 1FDJ 2FP 3.34448
43 1EIX BMQ 3.67347
44 3B1Q NOS 3.67893
45 4R74 F6P 3.67893
46 1VRP ADP 3.67893
47 5K8B PDG 3.67893
48 4Z5W TYS ILE TYS THR GLN 3.67893
49 1XTT U5P 3.7037
50 2CJF RP4 3.82166
51 3MKH FAD 4.01338
52 2ZZV LAC 4.01338
53 1DL5 SAH 4.34783
54 2VAR KDF 4.34783
55 2VAR KDG 4.34783
56 2I6A 5I5 4.34783
57 3KRL KRL 4.34783
58 4X7G NAP 4.38247
59 5V13 JH3 4.51389
60 1QF9 ADP 4.63918
61 1QF9 ALF 4.63918
62 1QF9 C5P 4.63918
63 2C49 ADN 4.68227
64 3OTX AP5 4.68227
65 6GBC AMP 4.68227
66 5EUD 5S6 4.68227
67 3LU1 NAD 4.68227
68 2HCJ GDP 4.68227
69 4OUC 5ID 4.68227
70 3F5O UOC COA 4.72973
71 3LOO B4P 5.01672
72 1Y9G FRU 5.01672
73 4CCK OGA 5.01672
74 5XVG 8FX 5.11945
75 5JCA FAD 5.28169
76 4C1K PEP 5.34351
77 2BME GNP 5.37634
78 4O6W ACE PRO LEU 2SO SER TPO NH2 5.48523
79 1PNO NAP 5.55556
80 4DSG FAD 5.68562
81 4DSG UDP 5.68562
82 1P3D ANP 5.68562
83 1GQY ACP 5.68562
84 2Z7R STU 5.68562
85 5XET ME8 5.68562
86 4OH4 ANP 5.68562
87 3N8K D1X 5.81395
88 4R81 FMN 5.82524
89 4P6X HCY 5.88235
90 5DI3 GNP 5.94595
91 1GSA ADP 6.02007
92 5IKI A9H 6.02007
93 1EUS DAN 6.02007
94 5ZI2 NAD 6.02007
95 3WCS MAN NAG GAL 6.29921
96 1W5T ANP 6.35452
97 2XGT NSS 6.35452
98 3EXH TPP 6.5445
99 4YEE 4CQ 6.66667
100 2X06 NAD 6.68896
101 4WAS COO 6.68896
102 5XNC N4P 7.02341
103 4EMV 0R9 7.07965
104 2XD9 XD9 7.18563
105 5EEH SAH 8.02676
106 2CXG GLC G6D ACI GLC 8.02676
107 2YAJ 4HP 8.13953
108 2GJ8 ALF GDP 8.13953
109 1UGX GAL MGC 8.27068
110 3O0Q GDP 8.3612
111 3O0Q TTP 8.3612
112 3O0Q ADN 8.3612
113 3ZKI WZV 8.3612
114 1F5F DHT 8.78049
115 1G8K MGD 9.02256
116 2IVN ANP 9.0301
117 5O0J GLC 9.0301
118 2C2A ADP 9.30233
119 1KZN CBN 10.2439
120 1O5O U5P 10.4072
121 1LSS NAD 11.4286
122 1Q8A HCS 12.709
123 3BOF HCS 12.709
124 4QYS PLR 14.0468
125 6C7Y ADP 17.094
Pocket No.: 2; Query (leader) PDB : 4GNC; Ligand: ASO; Similar sites found with APoc: 71
This union binding pocket(no: 2) in the query (biounit: 4gnc.bio2) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 2P3C 3TL None
2 2FXD DR7 None
3 2P3B 3TL None
4 1W2D 4IP 1.13208
5 4P5F AR6 1.33779
6 2RHW C0E 1.76678
7 3VPC ADP 1.77305
8 1YOE RIB 2.00669
9 3FV3 IVA VAL VAL STA ALA STA 2.00669
10 5DOZ NDP 2.00669
11 1XON PIL 2.00669
12 2AQX ATP 2.07612
13 2GQR ADP 2.1097
14 5AYE BMA BMA 2.34114
15 1I52 CTP 2.54237
16 3KF3 FRU 2.67559
17 3P7N FMN 2.71318
18 1W2T SUC GLA 3.01003
19 2OVW CBI 3.01003
20 3L24 GOA 3.01003
21 3OA2 NAD 3.01003
22 3S43 478 3.0303
23 4CYD CMP 3.11111
24 4ORR PE3 3.15789
25 3R35 4CO 3.31126
26 3IU9 T07 3.47222
27 4IKR PVP 3.67893
28 5Z5I XYS 3.67893
29 5Z5I FUB 3.67893
30 2Q7D ANP 3.67893
31 4YRD 3IT 3.67893
32 2MAS PIR 4.01338
33 1R5L VIV 4.19847
34 2H6T IVA VAL VAL STA ALA STA 4.34783
35 2QJY SMA 4.46097
36 1UZD CAP 4.47761
37 5GWT NAD 4.67626
38 3MKN DNB 5.01672
39 2D3N GLC GLC GLC GLC 5.01672
40 2D3N GLC 5.01672
41 2D3N GLC GLC GLC GLC GLC GLC 5.01672
42 2PZI AXX 5.01672
43 4CVC PQQ 5.35117
44 2GQS ADP 5.48523
45 2Y7G AAE 5.67376
46 5ZZA LAB 5.68562
47 2GSU AMP 6.02007
48 2OQ2 A3P 6.13027
49 1PG4 COA 6.35452
50 1PG4 PRX 6.35452
51 3X01 AMP 6.35452
52 3SXN COA 6.68896
53 5VFC 9BA 7.02341
54 1ZM1 BGC BGC BGC 7.05394
55 3VPB ADP 7.14286
56 1Z2P I3S 7.69231
57 1Z2P ACP 7.69231
58 3EPW JMQ 8.02676
59 4NDN SAM 8.02676
60 2V63 CAP 9.28571
61 2VDH CAP 9.28571
62 4YHQ G10 10.101
63 1U0A BGC BGC BGC BGC 11.215
64 1UMD TDP COI 11.3712
65 2PR5 FMN 12.1212
66 5DKK FMN 13.1034
67 4QYS PLP SEP 14.0468
68 2Z6C FMN 14.7287
69 2Z6D FMN 17.6923
70 2GVV DI9 18.7291
71 3GM5 CIT 23.8994
Pocket No.: 3; Query (leader) PDB : 4GNC; Ligand: ASO; Similar sites found with APoc: 36
This union binding pocket(no: 3) in the query (biounit: 4gnc.bio2) has 7 residues
No: Leader PDB Ligand Sequence Similarity
1 4ZLU ADP 1.33779
2 3GFS FMN 1.72414
3 6BCB GSP 2.16216
4 1G6O ADP 2.34114
5 4MO4 ACP 2.42588
6 3LXK MI1 2.67559
7 4X9X OLA 2.67559
8 2B3D FAD 2.94118
9 1WD4 AHR 3.01003
10 3AKI AH8 3.34448
11 5JZJ AN2 3.367
12 5D63 FUC GAL GLA 3.41297
13 5D9J 0N8 3.74332
14 5HDJ FMN 3.89105
15 5GM1 SAH 4.0404
16 3PE2 E1B 4.34783
17 3A23 GAL 4.34783
18 6BCA GSP 4.63576
19 1V47 ADX 4.68227
20 5NUL FMN 5.07246
21 4EHU ANP 5.43478
22 4KIL 1R5 5.6338
23 5MRH Q9Z 6.02007
24 4C0X FMN 6.89655
25 4C0X AQN 6.89655
26 3VC1 SAH 7.35786
27 3VC1 GST 7.35786
28 3N2S FMN 7.63052
29 4NBI D3Y 9.14634
30 3TAY MN0 9.81595
31 2QBU SAH 9.91379
32 2Z9C DTC 10
33 2Z9C FMN 10
34 1XKW 188 10.0334
35 1NTV ASN PHE ASP ASN PRO VAL TYR ARG LYS THR 11.8421
36 1T5B FMN 12.4378
Pocket No.: 4; Query (leader) PDB : 4GNC; Ligand: ASO; Similar sites found with APoc: 85
This union binding pocket(no: 4) in the query (biounit: 4gnc.bio1) has 7 residues
No: Leader PDB Ligand Sequence Similarity
1 1MFG GLU TYR LEU GLY LEU ASP VAL PRO VAL None
2 4UP3 FAD 1.33779
3 3ITJ FAD 1.67224
4 2JEN GLC GLC XYS XYS 1.91571
5 1VA6 ADP 2.00669
6 1VA6 P2S 2.00669
7 1ON3 MCA 2.00669
8 5HK9 64O 2.00669
9 4RI6 GSH 2.32558
10 4EU7 COA 2.34114
11 4EU7 CIT 2.34114
12 5JFL NAD 2.34114
13 5V7I 8Z1 2.34114
14 1QXO FMN 2.34114
15 6G1P CIT 2.34114
16 5GVL PLG 2.67559
17 5GVL GI8 2.67559
18 3LAD FAD 2.67559
19 1U8X NAD 2.67559
20 2QFY AKG 2.67559
21 2ZWI C5P 2.67559
22 3B0P FMN 2.67559
23 1AXD GGL CYW GLY 2.87081
24 5TUK FAD 3.01003
25 1EZ0 NAP 3.01003
26 4WZ8 3W7 3.01003
27 5LD8 6U5 3.21839
28 3IP6 PRO 3.34448
29 4A3U FMN 3.34448
30 2RI1 GLP 3.40426
31 4JSR 1NQ 3.50877
32 3UCL NAP 3.67893
33 1OX5 1PR 3.67893
34 3KFL ME8 3.67893
35 3VC3 C6P 3.67893
36 1JQ3 AAT 3.71622
37 5A4W QCT 3.77358
38 4K81 GTP 3.87597
39 1VYP FMN 4.01338
40 1VYP TNF 4.01338
41 1NB9 RBF 4.08163
42 1NB9 ADP 4.08163
43 6F05 GTS 4.18605
44 2DXU BT5 4.25532
45 3ZQ6 ADP ALF 4.34783
46 5WPJ NDP 4.68227
47 6G34 5ID 4.68227
48 5EY9 5SV 4.68227
49 3GE7 AFQ 4.68227
50 4NZ6 DGL 4.68227
51 5M06 ADP 4.71014
52 2F5X ASP 4.80769
53 1DFO FFO 5.01672
54 5TVA AMP 5.41667
55 1BKC INN 5.46875
56 3TCT 3MI 5.51181
57 2WET FAD 5.68562
58 4IP7 FBP 6.02007
59 1JZS MRC 6.68896
60 1MJT NAD 6.68896
61 5ALC TIQ 6.83761
62 3GBR PRP 7.24638
63 1EWK GLU 7.35786
64 4NDO ATP 7.77778
65 3SJK LYS PRO VAL LEU ARG THR ALA 7.89474
66 5F05 GSH 8.01887
67 1D1T NAD 8.02676
68 5JE8 NAD 8.02676
69 1V2X SAM 8.24742
70 3NK7 SAM 8.30325
71 3WO0 ADP 8.3612
72 3WO0 ALA 8.3612
73 4GNI ATP 8.69565
74 5ITZ GDP 8.69565
75 4ZB6 GDS 10.7623
76 1DAK ADP 12.9464
77 1DAK DPU 12.9464
78 1NC2 DOE 14.4186
79 1NC4 DOF 14.4186
80 5O96 SAM 14.6939
81 5CCM SAM 21.0702
82 5CCM 4ZX 21.0702
83 5N53 8NB 21.5385
84 3H0L ADP 24.4681
85 1WN3 HXC 30.1471
Pocket No.: 5; Query (leader) PDB : 4GNC; Ligand: ASO; Similar sites found with APoc: 28
This union binding pocket(no: 5) in the query (biounit: 4gnc.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 1W2D ADP 1.13208
2 5NE5 KIF 1.67224
3 3LDW ZOL 1.67224
4 2P9H IPT 1.85874
5 3GWT 066 2.00669
6 3KMZ EQO 2.25564
7 4NMC FAD 2.34114
8 4XOE KGM 2.50896
9 1R18 SAH 2.64317
10 5EQY 5RA 2.67559
11 1TIP F6P 3.14136
12 2YFT DQR 3.34448
13 5N5S NAP 3.67893
14 3ORF NAD 3.98406
15 4UTG ANP 4.34783
16 5CSD ACD 4.40252
17 1UZH CAP 4.91803
18 1AUX AGS 5.01672
19 1QXW M1C 5.15873
20 3KV8 FAH 5.7554
21 5JNN 6LM 5.78947
22 6MPT C30 5.94406
23 1N62 FAD 6.25
24 1X0P FAD 6.29371
25 1YKD CMP 10.0334
26 2C94 TSF 10.625
27 2E3N 6CM 13.7255
28 6MFL OPV 20.7358
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