Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SA0 A:501;
B:501;
 Valid;
Valid;
 none;
none;
 submit data
286.278 C13 H18 O7 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: SA0; Similar ligands found: 23
No: Ligand ECFP6 Tc MDL keys Tc
1 SA0 1 1
2 6GR 0.57377 0.918919
3 145 0.564516 0.62963
4 56N 0.535714 0.942857
5 MHD GAL 0.5 0.62963
6 3X8 0.47619 0.891892
7 GAT 0.474576 0.785714
8 GAA 0.447761 0.611111
9 GLA BEZ 0.447761 0.891892
10 GAL PHB 0.444444 0.916667
11 PNA 0.430769 0.622642
12 PNW 0.430769 0.622642
13 GLA NPO 0.430769 0.622642
14 MBE 0.430769 0.622642
15 147 0.430769 0.622642
16 NBZ GLA 0.430769 0.622642
17 PNG 0.430769 0.622642
18 XMM 0.430556 0.653846
19 CWK 0.418919 0.772727
20 HNW 0.41791 0.918919
21 EJN 0.405797 0.829268
22 ZZ1 GAL 0.405405 0.809524
23 5U7 0.405063 0.7
Similar Ligands (3D)
Ligand no: 1; Ligand: SA0; Similar ligands found: 82
No: Ligand Similarity coefficient
1 IFM BGC 0.9521
2 9MR 0.9458
3 BGC BGC 0.9399
4 BGC OXZ 0.9332
5 BMA BGC 0.9246
6 NOY BGC 0.9245
7 BMA IFM 0.9109
8 GMP 0.9103
9 XYP XIF 0.9097
10 IFM BMA 0.9092
11 XIF XYP 0.9089
12 6EN 0.9072
13 BGC GAL 0.9054
14 SHG BGC 0.9053
15 2FA 0.9048
16 PA1 GCS 0.9046
17 ADN 0.9039
18 FYJ 0.9013
19 CMU 0.9010
20 43S 0.8994
21 4GU 0.8980
22 5ID 0.8972
23 TLF 0.8969
24 ISX 0.8966
25 AD3 0.8966
26 GCS GCS 0.8963
27 38B 0.8932
28 C0H 0.8926
29 17C 0.8925
30 ID8 0.8922
31 FLF 0.8919
32 IMG 0.8900
33 7NU 0.8892
34 LI4 0.8872
35 XYP XYP 0.8866
36 EKH 0.8865
37 4L2 0.8863
38 6CR 0.8863
39 636 0.8862
40 NOS 0.8861
41 GLO BGC 0.8859
42 U19 0.8852
43 MFR 0.8842
44 3WJ 0.8841
45 XDN XYP 0.8830
46 XYP XDN 0.8827
47 TCC 0.8819
48 FTU 0.8813
49 1FL 0.8812
50 MG7 0.8803
51 XDL XYP 0.8795
52 7W7 0.8788
53 4E5 0.8787
54 5JT 0.8778
55 HMD 0.8764
56 XIL 0.8719
57 XYP AHR 0.8717
58 683 0.8708
59 GN6 0.8687
60 SGP 0.8686
61 CQW 0.8677
62 9CE 0.8676
63 DBQ 0.8676
64 CJZ 0.8675
65 XYP XYS 0.8668
66 RFZ 0.8648
67 XZ8 0.8638
68 3Y7 0.8621
69 A4G 0.8620
70 CL9 0.8612
71 1ZC 0.8601
72 GAL FUC 0.8596
73 M02 0.8594
74 FHI 0.8578
75 MBY 0.8576
76 22L 0.8576
77 CC5 0.8573
78 2LX 0.8570
79 5NB 0.8569
80 RGG 0.8557
81 6J9 0.8557
82 BQZ 0.8527
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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