Receptor
PDB id Resolution Class Description Source Keywords
6RK2 2.09 Å EC: 3.2.1.21 COMPLEX STRUCTURE OF VIRULENCE FACTOR SGHA MUTANT WITH ITS S SAG AGROBACTERIUM TUMEFACIENS A6 CHEMICAL SIGNALING SUCROSE AGROBACTERIUM HOST-PATHOGEN INTERACTION GLUCOSIDASE HYDROLASE
Ref.: AGROBACTERIA REPROGRAM VIRULENCE GENE EXPRESSION BY CONTROLLED RELEASE OF HOST-CONJUGATED SIGNALS. PROC.NATL.ACAD.SCI.USA V. 116 22331 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
6GR B:501;
A:501;
 Valid;
Valid;
 none;
none;
 submit data
300.261 C13 H16 O8 c1ccc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6RJO 1.8 Å EC: 3.2.1.21 COMPLEX STRUCTURE OF VIRULENCE FACTOR SGHA WITH ITS SUBSTRAT SALICIN AGROBACTERIUM TUMEFACIENS A6 CHEMICAL SIGNALING SUCROSE AGROBACTERIUM HOST-PATHOGEN INTERACTION GLUCOSIDASE HYDROLASE
Ref.: AGROBACTERIA REPROGRAM VIRULENCE GENE EXPRESSION BY CONTROLLED RELEASE OF HOST-CONJUGATED SIGNALS. PROC.NATL.ACAD.SCI.USA V. 116 22331 2019
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 25 families.
1 6RJM - GLC C6 H12 O6 C([C@@H]1[....
2 6RK2 - 6GR C13 H16 O8 c1ccc(c(c1....
3 6RJO - SA0 C13 H18 O7 c1ccc(c(c1....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 6RJM - GLC C6 H12 O6 C([C@@H]1[....
2 6RK2 - 6GR C13 H16 O8 c1ccc(c(c1....
3 6RJO - SA0 C13 H18 O7 c1ccc(c(c1....
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: 6GR; Similar ligands found: 22
No: Ligand ECFP6 Tc MDL keys Tc
1 6GR 1 1
2 SA0 0.57377 0.918919
3 145 0.553846 0.648148
4 GLA BEZ 0.507463 0.918919
5 56N 0.5 0.916667
6 GAA 0.463768 0.62963
7 GAL PHB 0.461538 0.944444
8 3XJ 0.45 0.686275
9 3X8 0.447761 0.868421
10 GAT 0.444444 0.767442
11 SBQ 0.433735 0.777778
12 XMM 0.426667 0.641509
13 MBE 0.426471 0.641509
14 PNW 0.426471 0.641509
15 147 0.426471 0.641509
16 GLA NPO 0.426471 0.641509
17 PNG 0.426471 0.641509
18 PNA 0.426471 0.641509
19 NBZ GLA 0.426471 0.641509
20 ZZ1 GAL 0.421053 0.833333
21 5U7 0.419753 0.686275
22 AI1 0.419753 0.73913
Similar Ligands (3D)
Ligand no: 1; Ligand: 6GR; Similar ligands found: 38
No: Ligand Similarity coefficient
1 ISX 0.9134
2 9MR 0.8982
3 BGC OXZ 0.8966
4 IFM BGC 0.8963
5 6EN 0.8944
6 ID8 0.8927
7 BGC BGC 0.8908
8 TLF 0.8901
9 6J3 0.8893
10 GLC GAL 0.8879
11 43S 0.8858
12 5ID 0.8849
13 BGC GAL 0.8824
14 7CI 0.8821
15 17C 0.8817
16 SGV 0.8817
17 GLC BGC 0.8808
18 M2F 0.8797
19 LI4 0.8793
20 OFL 0.8790
21 GCS GCS 0.8775
22 EKH 0.8764
23 BMA IFM 0.8752
24 FTU 0.8747
25 HO4 0.8739
26 IFM BMA 0.8739
27 636 0.8724
28 683 0.8711
29 MG7 0.8711
30 5E4 0.8640
31 XYP AHR 0.8638
32 GN6 0.8621
33 F01 0.8607
34 FNA 0.8594
35 EZB 0.8572
36 3B4 0.8566
37 XYP XIF 0.8546
38 BGC BMA 0.8535
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6RJO; Ligand: SA0; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 6rjo.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6RJO; Ligand: SA0; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 6rjo.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
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