Receptor
PDB id Resolution Class Description Source Keywords
5YIF 2.45 Å EC: 7.-.-.- PYRUVYLATED BETA-D-GALACTOSIDASE FROM BACILLUS SP. HMA207, E MUTANT PYRUVYLATED BETA-D-GALACTOSE COMPLEX BACILLUS SP. GLYCOSIDE HYDROLASE HYDROLASE
Ref.: IDENTIFICATION AND CHARACTERIZATION OF A NOVEL BETA-D-GALACTOSIDASE THAT RELEASES PYRUVYLATED GALA SCI REP V. 8 12013 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
8VR B:501;
A:501;
 Valid;
Valid;
 none;
none;
 submit data
250.203 C9 H14 O8 C[C@]...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5YIF 2.45 Å EC: 7.-.-.- PYRUVYLATED BETA-D-GALACTOSIDASE FROM BACILLUS SP. HMA207, E MUTANT PYRUVYLATED BETA-D-GALACTOSE COMPLEX BACILLUS SP. GLYCOSIDE HYDROLASE HYDROLASE
Ref.: IDENTIFICATION AND CHARACTERIZATION OF A NOVEL BETA-D-GALACTOSIDASE THAT RELEASES PYRUVYLATED GALA SCI REP V. 8 12013 2018
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 319 families.
1 5YIF - 8VR C9 H14 O8 C[C@]1(OC[....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 271 families.
1 5YIF - 8VR C9 H14 O8 C[C@]1(OC[....
50% Homology Family (89)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1W9D ic50 = 0.58 mM SEH C10 H13 N O4 S2 CCS/C(=NOS....
2 1W9B ic50 = 0.99 mM CGT C15 H21 N O8 S2 c1ccc(cc1)....
3 1E6Q Ki = 0.7 mM NTZ C6 H10 N4 O4 C([C@@H]1[....
4 1E70 - G2F C6 H11 F O5 C([C@@H]1[....
5 1E71 - ASC C6 H8 O6 C([C@@H]([....
6 2WXD ic50 = 3.3 uM E18 C12 H18 N2 O4 S2 CN(C)CCS/C....
7 1E72 Ki = 0.6 mM GOX C6 H12 N2 O5 C([C@@H]1[....
8 1E6X - LGC C6 H10 O6 C([C@@H]1[....
9 1E73 - ASC C6 H8 O6 C([C@@H]([....
10 1E6S Ki = 0.6 mM GOX C6 H12 N2 O5 C([C@@H]1[....
11 1BGG - GCO C6 H12 O7 C([C@H]([C....
12 6R4K Ki = 51 uM JSK C17 H25 N7 O4 [H]/N=N/NC....
13 1E4I - NFG C12 H13 F N2 O9 c1cc(c(cc1....
14 4EK7 - BGC C6 H12 O6 C([C@@H]1[....
15 3U57 - DH8 C27 H34 N2 O8 C/C=C/1[C@....
16 3U5Y - SCG C17 H24 O10 COC(=O)C1=....
17 5OKK - BGP C6 H13 O9 P C([C@@H]1[....
18 5OKE - BG6 C6 H13 O9 P C([C@@H]1[....
19 5OKR - BG6 C6 H13 O9 P C([C@@H]1[....
20 5OKG - BG6 C6 H13 O9 P C([C@@H]1[....
21 5OKQ - BGP C6 H13 O9 P C([C@@H]1[....
22 5OKS - BG6 C6 H13 O9 P C([C@@H]1[....
23 2ZOX - OLA C18 H34 O2 CCCCCCCCC=....
24 2E9M - OLA C18 H34 O2 CCCCCCCCC=....
25 2E9L - OLA C18 H34 O2 CCCCCCCCC=....
26 3AI0 - PNW C12 H15 N O8 c1cc(ccc1[....
27 4IPN - SGC RTG n/a n/a
28 5N6T - 8P2 C7 H11 N2 O4 C([C@@H]1[....
29 2WBG Ki = 35.2 uM LGS C15 H28 N2 O5 CCCCCCCC/N....
30 2J7H Kd = 65 nM AZF C5 H12 N2 O3 C1[C@H]([C....
31 2J7D Kd = 74 nM GI1 C10 H17 N2 O6 CO[C@@H](c....
32 1W3J Kd = 484 nM OXZ C5 H11 N O4 C1[C@H]([C....
33 2J7C Ki = 10.7 nM IDE C15 H19 N3 O4 c1ccc(cc1)....
34 2J79 Kd = 1.1 uM GTL C6 H12 N2 O5 C([C@@H]1[....
35 2WC3 Ki = 0.83 uM AM3 C15 H28 N2 O5 CCCCCCCC/N....
36 2J75 - NOY C6 H13 N O4 C1[C@@H]([....
37 2VRJ Kd = 0.5 uM NCW C15 H28 N2 O4 S CCCCCCCCNC....
38 2J7F Kd = 445 nM GI3 C9 H13 N2 O6 c1c([nH]c2....
39 2J77 Kd = 12.9 uM NOJ C6 H13 N O4 C1[C@@H]([....
40 5OSS Kd = 28.3 uM AEZ C8 H12 N2 O4 c1[nH]c2c(....
41 1UZ1 Ki = 130 nM IFL C6 H11 N O4 C1[C@@H]([....
42 2CBU Kd = 2.1 uM CTS C8 H15 N O4 C1C[N@]2C[....
43 2J7G Kd = 100 nM GI4 C10 H15 N2 O6 c1c([nH]c2....
44 5N6S - 8P5 C13 H23 N4 O5 C(CCN=[N+]....
45 2WC4 Kd = 5.1 uM AMF C15 H28 N2 O4 S CCCCCCCCN=....
46 2CBV Kd = 3.3 uM CGB C7 H13 N O4 C1C[C@]2([....
47 1OIF Ka = 51450000 M^-1 IFM C6 H13 N O3 C1[C@@H]([....
48 2CES Kd = 56 nM GIM C8 H13 N2 O4 c1c[n+]2c(....
49 2J7E Kd = 48 nM GI2 C11 H17 N2 O6 COC(=O)Cc1....
50 2J78 Kd = 384 nM GOX C6 H12 N2 O5 C([C@@H]1[....
51 1OIM Ka = 210000 M^-1 NOJ C6 H13 N O4 C1[C@@H]([....
52 2CET Kd = 9.6 nM PGI C16 H21 N2 O4 c1ccc(cc1)....
53 2J7B Kd = 240 nM NTZ C6 H10 N4 O4 C([C@@H]1[....
54 4JIE - BMA C6 H12 O6 C([C@@H]1[....
55 3AIV - HBO C9 H9 N O5 COc1ccc2c(....
56 3AIQ - HBO C9 H9 N O5 COc1ccc2c(....
57 3AIR - DNF C6 H4 N2 O5 c1cc(c(cc1....
58 3AIS - HBK BGC n/a n/a
59 3AIW - DNF C6 H4 N2 O5 c1cc(c(cc1....
60 4PTX - BGC C6 H12 O6 C([C@@H]1[....
61 4PTV - SGC BGC n/a n/a
62 3GNP - SOG C14 H28 O5 S CCCCCCCCS[....
63 6RJM - GLC C6 H12 O6 C([C@@H]1[....
64 6RK2 - 6GR C13 H16 O8 c1ccc(c(c1....
65 6RJO - SA0 C13 H18 O7 c1ccc(c(c1....
66 5AYI - BGC C6 H12 O6 C([C@@H]1[....
67 1E56 - BGC HBO n/a n/a
68 1E55 Ki = 76 uM DHR C8 H7 N O2 c1cc(ccc1[....
69 1V08 Ki ~ 1 uM NTZ C6 H10 N4 O4 C([C@@H]1[....
70 1E4N - HBO C9 H9 N O5 COc1ccc2c(....
71 1H49 - HBO BGC n/a n/a
72 5GNX - BGC C6 H12 O6 C([C@@H]1[....
73 5GNY - BGC C6 H12 O6 C([C@@H]1[....
74 5GNZ - BGC C6 H12 O6 C([C@@H]1[....
75 2E40 - LGC C6 H10 O6 C([C@@H]1[....
76 3F5K Ki = 0.024 mM BGC BGC BGC BGC BGC n/a n/a
77 7BZM - GIM C8 H13 N2 O4 c1c[n+]2c(....
78 4QLL Ka = 2400 M^-1 BGC BGC BGC BGC n/a n/a
79 4QLJ - BGC BGC BGC BGC n/a n/a
80 3F5J Ki = 0.052 mM BGC BGC BGC BGC n/a n/a
81 4QLK Ka = 1800 M^-1 BGC BGC BGC BGC n/a n/a
82 3F5L Ki = 0.191 mM BGC BGC n/a n/a
83 3PTQ - NFG C12 H13 F N2 O9 c1cc(c(cc1....
84 4PBG - BGP C6 H13 O9 P C([C@@H]1[....
85 3CMJ - SRT C4 H6 O6 [C@H]([C@H....
86 5YIF - 8VR C9 H14 O8 C[C@]1(OC[....
87 1V03 - BGC CCN IPH n/a n/a
88 2O9T - BGC C6 H12 O6 C([C@@H]1[....
89 2O9R Ki = 21 mM SGC BGC n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 8VR; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 8VR 1 1
2 CEG 1 1
3 46M 1 1
4 CDG 0.607143 0.864865
5 46D 0.536232 0.916667
6 6LA 0.515625 0.666667
Similar Ligands (3D)
Ligand no: 1; Ligand: 8VR; Similar ligands found: 68
No: Ligand Similarity coefficient
1 78U 0.9134
2 BGP 0.9092
3 G6P 0.9017
4 BG6 0.9017
5 KYN 0.8941
6 CIP 0.8891
7 XYH 0.8885
8 JF1 0.8877
9 YOF 0.8864
10 TRP 0.8837
11 GC3 0.8826
12 2K8 0.8818
13 30G 0.8804
14 TOH 0.8801
15 DAH 0.8801
16 V1T 0.8793
17 IYR 0.8790
18 0JD 0.8787
19 GLP 0.8779
20 9FQ 0.8769
21 ZYQ 0.8749
22 5TY 0.8748
23 57O 0.8748
24 LIP 0.8748
25 4OG 0.8734
26 EXL 0.8726
27 TYR 0.8710
28 HBO 0.8706
29 092 0.8700
30 ICB 0.8692
31 MUR 0.8685
32 IOS 0.8682
33 JVN 0.8680
34 0FK 0.8674
35 SIZ 0.8660
36 TLM 0.8659
37 BY5 0.8657
38 X1P 0.8656
39 PMP 0.8648
40 ZON 0.8648
41 DCZ 0.8637
42 THM 0.8635
43 MP5 0.8632
44 PLP 0.8631
45 8W9 0.8628
46 94E 0.8627
47 IOP 0.8626
48 IPD 0.8625
49 U2Z 0.8621
50 KTW 0.8615
51 GF1 0.8613
52 QUS 0.8612
53 9BF 0.8610
54 5JT 0.8584
55 CMU 0.8576
56 M3Q 0.8569
57 HHS 0.8560
58 RGY 0.8557
59 S3C 0.8554
60 F6R 0.8548
61 DUR 0.8545
62 7MK 0.8544
63 PHE 0.8541
64 68A 0.8537
65 AP4 0.8530
66 9KH 0.8508
67 MXD 0.8507
68 9PL 0.8502
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5YIF; Ligand: 8VR; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 5yif.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 2CER PGI 42.5263
2 2CER PGI 42.5263
Pocket No.: 2; Query (leader) PDB : 5YIF; Ligand: 8VR; Similar sites found with APoc: 2
This union binding pocket(no: 2) in the query (biounit: 5yif.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 2CER PGI 42.5263
2 2CER PGI 42.5263
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