Receptor
PDB id Resolution Class Description Source Keywords
6PMF 1.95 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF ECDSBA IN COMPLEX WITH ANILINE 15 ESCHERICHIA COLI (STRAIN K12) DISULFIDE OXIDOREDUCTASE REDOX PROTEIN OXIDOREDUCTASE-INHICOMPLEX OXIDOREDUCTASE
Ref.: THE FRAGMENT-BASED DEVELOPMENT OF A BENZOFURAN HIT CLASS OF ESCHERICHIA COLI DSBA INHIBITORS. MOLECULES V. 24 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CU B:201;
 Part of Protein;
 none;
 submit data
63.546 Cu [Cu+2...
LD9 A:201;
 Valid;
 none;
 submit data
267.279 C16 H13 N O3 c1ccc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6PDH 1.96 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF ECDSBA IN A COMPLEX WITH PURIFIED PYRAZ ESCHERICHIA COLI (STRAIN K12) DISULFIDE OXIDOREDUCTASE REDOX PROTEIN OXIDOREDUCTASE-INHICOMPLEX REFILX OXIDOREDUCTASE
Ref.: RAPID ELABORATION OF FRAGMENTS INTO LEADS BY X-RAY CRYSTALLOGRAPHIC SCREENING OF PARALLEL CHEMICAL LIB (REFIL X ). J.MED.CHEM. V. 63 6863 2020
Members (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 6PD7 Kd = 290 uM OAJ C21 H20 N2 O5 Cc1cc(ccc1....
2 6PBI Kd = 365 uM O6Y C20 H20 N2 O3 Cc1cc(ccc1....
3 6PVZ Kd = 341 uM OZM C17 H14 O3 c1ccc(cc1)....
4 6PLI Kd = 230 uM ONY C22 H22 N4 O3 Cc1cc(ccc1....
5 6PML Kd = 820 uM OR4 C17 H14 O4 c1ccc(cc1)....
6 6PDH Kd = 62 uM OAV C23 H24 N4 O2 CCN(CCn1cc....
7 6BR4 - 60L C12 H13 N S CNCc1cccc(....
8 4ZIJ Kd = 565 uM SFQ C13 H10 I N O4 S c1ccc(c(c1....
9 6PMF - LD9 C16 H13 N O3 c1ccc(cc1)....
10 4WF4 Kd = 777 uM WF4 C12 H8 F3 N O2 S Cc1c(sc(n1....
11 6WHD Kd = 490 uM KFS C16 H13 N O3 Cc1cc(ccc1....
12 4WET Kd = 444 uM WEF C21 H17 F3 N2 O4 S Cc1c(sc(n1....
13 6PGJ - OAJ C21 H20 N2 O5 Cc1cc(ccc1....
14 6PC9 Kd = 480 uM O7P C21 H21 N3 O3 Cc1cc(ccc1....
15 6POQ Kd = 2700 uM OVJ C17 H15 N O4 COc1ccc(cc....
16 6BQX - 9AG C14 H15 N O CNCc1ccc(c....
17 4WF5 Kd = 777 uM WF4 C12 H8 F3 N O2 S Cc1c(sc(n1....
18 6PG1 - O7P C21 H21 N3 O3 Cc1cc(ccc1....
19 6PIQ - OAV C23 H24 N4 O2 CCN(CCn1cc....
20 6POI Kd = 326 uM OVS C16 H12 O4 c1ccc(cc1)....
21 6PG2 - O6Y C20 H20 N2 O3 Cc1cc(ccc1....
22 6PVY Kd = 639 uM OZG C17 H14 O5 COc1cccc(c....
23 4WEY Kd = 318 uM EG6 C15 H13 F3 N2 O4 S Cc1c(sc(n1....
24 6POH Kd = 1970 uM OVG C14 H16 O4 CCCCOc1ccc....
70% Homology Family (25)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 6PD7 Kd = 290 uM OAJ C21 H20 N2 O5 Cc1cc(ccc1....
2 6PBI Kd = 365 uM O6Y C20 H20 N2 O3 Cc1cc(ccc1....
3 6PVZ Kd = 341 uM OZM C17 H14 O3 c1ccc(cc1)....
4 6PLI Kd = 230 uM ONY C22 H22 N4 O3 Cc1cc(ccc1....
5 6PML Kd = 820 uM OR4 C17 H14 O4 c1ccc(cc1)....
6 6PDH Kd = 62 uM OAV C23 H24 N4 O2 CCN(CCn1cc....
7 6BR4 - 60L C12 H13 N S CNCc1cccc(....
8 4ZIJ Kd = 565 uM SFQ C13 H10 I N O4 S c1ccc(c(c1....
9 6PMF - LD9 C16 H13 N O3 c1ccc(cc1)....
10 4WF4 Kd = 777 uM WF4 C12 H8 F3 N O2 S Cc1c(sc(n1....
11 6WHD Kd = 490 uM KFS C16 H13 N O3 Cc1cc(ccc1....
12 4WET Kd = 444 uM WEF C21 H17 F3 N2 O4 S Cc1c(sc(n1....
13 6PGJ - OAJ C21 H20 N2 O5 Cc1cc(ccc1....
14 6PC9 Kd = 480 uM O7P C21 H21 N3 O3 Cc1cc(ccc1....
15 6POQ Kd = 2700 uM OVJ C17 H15 N O4 COc1ccc(cc....
16 6BQX - 9AG C14 H15 N O CNCc1ccc(c....
17 4WF5 Kd = 777 uM WF4 C12 H8 F3 N O2 S Cc1c(sc(n1....
18 6PG1 - O7P C21 H21 N3 O3 Cc1cc(ccc1....
19 6PIQ - OAV C23 H24 N4 O2 CCN(CCn1cc....
20 6POI Kd = 326 uM OVS C16 H12 O4 c1ccc(cc1)....
21 6PG2 - O6Y C20 H20 N2 O3 Cc1cc(ccc1....
22 6PVY Kd = 639 uM OZG C17 H14 O5 COc1cccc(c....
23 4WEY Kd = 318 uM EG6 C15 H13 F3 N2 O4 S Cc1c(sc(n1....
24 6POH Kd = 1970 uM OVG C14 H16 O4 CCCCOc1ccc....
25 4OD7 - ACE PRO TRP ALA THR CYS ASP SER NH2 n/a n/a
50% Homology Family (25)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 6PD7 Kd = 290 uM OAJ C21 H20 N2 O5 Cc1cc(ccc1....
2 6PBI Kd = 365 uM O6Y C20 H20 N2 O3 Cc1cc(ccc1....
3 6PVZ Kd = 341 uM OZM C17 H14 O3 c1ccc(cc1)....
4 6PLI Kd = 230 uM ONY C22 H22 N4 O3 Cc1cc(ccc1....
5 6PML Kd = 820 uM OR4 C17 H14 O4 c1ccc(cc1)....
6 6PDH Kd = 62 uM OAV C23 H24 N4 O2 CCN(CCn1cc....
7 6BR4 - 60L C12 H13 N S CNCc1cccc(....
8 4ZIJ Kd = 565 uM SFQ C13 H10 I N O4 S c1ccc(c(c1....
9 6PMF - LD9 C16 H13 N O3 c1ccc(cc1)....
10 4WF4 Kd = 777 uM WF4 C12 H8 F3 N O2 S Cc1c(sc(n1....
11 6WHD Kd = 490 uM KFS C16 H13 N O3 Cc1cc(ccc1....
12 4WET Kd = 444 uM WEF C21 H17 F3 N2 O4 S Cc1c(sc(n1....
13 6PGJ - OAJ C21 H20 N2 O5 Cc1cc(ccc1....
14 6PC9 Kd = 480 uM O7P C21 H21 N3 O3 Cc1cc(ccc1....
15 6POQ Kd = 2700 uM OVJ C17 H15 N O4 COc1ccc(cc....
16 6BQX - 9AG C14 H15 N O CNCc1ccc(c....
17 4WF5 Kd = 777 uM WF4 C12 H8 F3 N O2 S Cc1c(sc(n1....
18 6PG1 - O7P C21 H21 N3 O3 Cc1cc(ccc1....
19 6PIQ - OAV C23 H24 N4 O2 CCN(CCn1cc....
20 6POI Kd = 326 uM OVS C16 H12 O4 c1ccc(cc1)....
21 6PG2 - O6Y C20 H20 N2 O3 Cc1cc(ccc1....
22 6PVY Kd = 639 uM OZG C17 H14 O5 COc1cccc(c....
23 4WEY Kd = 318 uM EG6 C15 H13 F3 N2 O4 S Cc1c(sc(n1....
24 6POH Kd = 1970 uM OVG C14 H16 O4 CCCCOc1ccc....
25 4OD7 - ACE PRO TRP ALA THR CYS ASP SER NH2 n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: LD9; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 LD9 1 1
2 OVJ 0.714286 0.864865
3 MQB 0.516667 0.6875
4 OZM 0.5 0.75
5 OVS 0.492958 0.666667
6 MS0 0.484848 0.605263
7 OR4 0.466667 0.631579
8 OZG 0.405063 0.631579
Similar Ligands (3D)
Ligand no: 1; Ligand: LD9; Similar ligands found: 26
No: Ligand Similarity coefficient
1 4UE 0.8974
2 OVG 0.8942
3 UV4 0.8929
4 LZ7 0.8900
5 JMM 0.8852
6 30A 0.8849
7 R3S 0.8847
8 1GO 0.8798
9 5NR 0.8794
10 AT2 0.8780
11 GOW 0.8766
12 BMU 0.8754
13 J9G 0.8751
14 FDZ 0.8749
15 16J 0.8716
16 GJW 0.8699
17 KVD 0.8670
18 1V6 0.8662
19 DP8 0.8661
20 S1C 0.8659
21 F13 0.8641
22 SU7 0.8639
23 4WA 0.8631
24 NAR 0.8630
25 DN8 0.8582
26 IXG 0.8581
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6PDH; Ligand: OAV; 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: 6pdh.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
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