Receptor
PDB id Resolution Class Description Source Keywords
1JHO 2 Å EC: 2.4.2.21 THREE-DIMENSIONAL STRUCTURE OF COBT IN COMPLEX WITH THE REAC PRODUCTS OF 5-METHYLBENZIMIDAZOLE AND NAMN SALMONELLA ENTERICA COBT COBALAMIN BIOSYNTHESIS LOWER LIGAND COBAMIDES NN:DBN1-ALPHA-PHOSPHORIBOSYLTRANSFERASE TRANSFERASE
Ref.: STRUCTURAL INVESTIGATION OF THE BIOSYNTHESIS OF ALT LOWER LIGANDS FOR COBAMIDES BY NICOTINATE MONONUCLE 5,6-DIMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE SALMONELLA ENTERICA. J.BIOL.CHEM. V. 276 37612 2001
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NIO A:991;
Valid;
none;
submit data
123.109 C6 H5 N O2 c1cc(...
RMB A:990;
Valid;
none;
submit data
344.257 C13 H17 N2 O7 P Cc1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4KQI 1.4 Å EC: 2.4.2.21 CRYSTAL STRUCTURE OF COBT E317A COMPLEXED WITH ITS REACTION SALMONELLA ENTERICA SUBSP. ENTERICA SETYPHIMURIUM TRANSFERASE
Ref.: DISSECTING COBAMIDE DIVERSITY THROUGH STRUCTURAL AN FUNCTIONAL ANALYSES OF THE BASE-ACTIVATING COBT ENZ SALMONELLA ENTERICA. BIOCHIM.BIOPHYS.ACTA V.1840 464 2014
Members (31)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1L4G - NCN C11 H14 N O9 P c1cc(c[n+]....
2 1D0S - DMD C9 H10 N2 Cc1cc2c(cc....
3 1L4K - NCN C11 H14 N O9 P c1cc(c[n+]....
4 4KQF - ADE C5 H5 N5 c1[nH]c2c(....
5 4KQJ - PCR C7 H8 O Cc1ccc(cc1....
6 1L4F - NCN C11 H14 N O9 P c1cc(c[n+]....
7 1JHV - PCR C7 H8 O Cc1ccc(cc1....
8 4KQG - DMD C9 H10 N2 Cc1cc2c(cc....
9 1L4N - NIO C6 H5 N O2 c1cc(cnc1)....
10 1JHM - 5MB C8 H8 N2 Cc1ccc2c(c....
11 1JHU - PCR C7 H8 O Cc1ccc(cc1....
12 1JH8 - ADE C5 H5 N5 c1[nH]c2c(....
13 1L4M - NCN C11 H14 N O9 P c1cc(c[n+]....
14 1L5L - NIO C6 H5 N O2 c1cc(cnc1)....
15 1L4L - XYD C8 H11 N Cc1ccc(c(c....
16 1JHQ - PMO C13 H17 N2 O8 P COc1ccc2c(....
17 1L5K - NIO C6 H5 N O2 c1cc(cnc1)....
18 1JHP - 5OB C8 H8 N2 O COc1ccc2c(....
19 1JHY - NIO C6 H5 N O2 c1cc(cnc1)....
20 1L5M - NIO C6 H5 N O2 c1cc(cnc1)....
21 1JHA - NIO C6 H5 N O2 c1cc(cnc1)....
22 1JHX - IPH C6 H6 O c1ccc(cc1)....
23 1JHO - RMB C13 H17 N2 O7 P Cc1ccc2c(c....
24 1JHR - P2P C10 H13 N4 O8 P c1c2c(ncn2....
25 1L4E - RBZ C14 H19 N2 O7 P Cc1cc2c(cc....
26 4KQK - PCR C7 H8 O Cc1ccc(cc1....
27 1D0V - RBZ C14 H19 N2 O7 P Cc1cc2c(cc....
28 1L5O - NCN C11 H14 N O9 P c1cc(c[n+]....
29 1L5F - BZI C7 H6 N2 c1ccc2c(c1....
30 1L4H - NCN C11 H14 N O9 P c1cc(c[n+]....
31 4KQI - NIO C6 H5 N O2 c1cc(cnc1)....
70% Homology Family (31)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1L4G - NCN C11 H14 N O9 P c1cc(c[n+]....
2 1D0S - DMD C9 H10 N2 Cc1cc2c(cc....
3 1L4K - NCN C11 H14 N O9 P c1cc(c[n+]....
4 4KQF - ADE C5 H5 N5 c1[nH]c2c(....
5 4KQJ - PCR C7 H8 O Cc1ccc(cc1....
6 1L4F - NCN C11 H14 N O9 P c1cc(c[n+]....
7 1JHV - PCR C7 H8 O Cc1ccc(cc1....
8 4KQG - DMD C9 H10 N2 Cc1cc2c(cc....
9 1L4N - NIO C6 H5 N O2 c1cc(cnc1)....
10 1JHM - 5MB C8 H8 N2 Cc1ccc2c(c....
11 1JHU - PCR C7 H8 O Cc1ccc(cc1....
12 1JH8 - ADE C5 H5 N5 c1[nH]c2c(....
13 1L4M - NCN C11 H14 N O9 P c1cc(c[n+]....
14 1L5L - NIO C6 H5 N O2 c1cc(cnc1)....
15 1L4L - XYD C8 H11 N Cc1ccc(c(c....
16 1JHQ - PMO C13 H17 N2 O8 P COc1ccc2c(....
17 1L5K - NIO C6 H5 N O2 c1cc(cnc1)....
18 1JHP - 5OB C8 H8 N2 O COc1ccc2c(....
19 1JHY - NIO C6 H5 N O2 c1cc(cnc1)....
20 1L5M - NIO C6 H5 N O2 c1cc(cnc1)....
21 1JHA - NIO C6 H5 N O2 c1cc(cnc1)....
22 1JHX - IPH C6 H6 O c1ccc(cc1)....
23 1JHO - RMB C13 H17 N2 O7 P Cc1ccc2c(c....
24 1JHR - P2P C10 H13 N4 O8 P c1c2c(ncn2....
25 1L4E - RBZ C14 H19 N2 O7 P Cc1cc2c(cc....
26 4KQK - PCR C7 H8 O Cc1ccc(cc1....
27 1D0V - RBZ C14 H19 N2 O7 P Cc1cc2c(cc....
28 1L5O - NCN C11 H14 N O9 P c1cc(c[n+]....
29 1L5F - BZI C7 H6 N2 c1ccc2c(c1....
30 1L4H - NCN C11 H14 N O9 P c1cc(c[n+]....
31 4KQI - NIO C6 H5 N O2 c1cc(cnc1)....
50% Homology Family (31)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1L4G - NCN C11 H14 N O9 P c1cc(c[n+]....
2 1D0S - DMD C9 H10 N2 Cc1cc2c(cc....
3 1L4K - NCN C11 H14 N O9 P c1cc(c[n+]....
4 4KQF - ADE C5 H5 N5 c1[nH]c2c(....
5 4KQJ - PCR C7 H8 O Cc1ccc(cc1....
6 1L4F - NCN C11 H14 N O9 P c1cc(c[n+]....
7 1JHV - PCR C7 H8 O Cc1ccc(cc1....
8 4KQG - DMD C9 H10 N2 Cc1cc2c(cc....
9 1L4N - NIO C6 H5 N O2 c1cc(cnc1)....
10 1JHM - 5MB C8 H8 N2 Cc1ccc2c(c....
11 1JHU - PCR C7 H8 O Cc1ccc(cc1....
12 1JH8 - ADE C5 H5 N5 c1[nH]c2c(....
13 1L4M - NCN C11 H14 N O9 P c1cc(c[n+]....
14 1L5L - NIO C6 H5 N O2 c1cc(cnc1)....
15 1L4L - XYD C8 H11 N Cc1ccc(c(c....
16 1JHQ - PMO C13 H17 N2 O8 P COc1ccc2c(....
17 1L5K - NIO C6 H5 N O2 c1cc(cnc1)....
18 1JHP - 5OB C8 H8 N2 O COc1ccc2c(....
19 1JHY - NIO C6 H5 N O2 c1cc(cnc1)....
20 1L5M - NIO C6 H5 N O2 c1cc(cnc1)....
21 1JHA - NIO C6 H5 N O2 c1cc(cnc1)....
22 1JHX - IPH C6 H6 O c1ccc(cc1)....
23 1JHO - RMB C13 H17 N2 O7 P Cc1ccc2c(c....
24 1JHR - P2P C10 H13 N4 O8 P c1c2c(ncn2....
25 1L4E - RBZ C14 H19 N2 O7 P Cc1cc2c(cc....
26 4KQK - PCR C7 H8 O Cc1ccc(cc1....
27 1D0V - RBZ C14 H19 N2 O7 P Cc1cc2c(cc....
28 1L5O - NCN C11 H14 N O9 P c1cc(c[n+]....
29 1L5F - BZI C7 H6 N2 c1ccc2c(c1....
30 1L4H - NCN C11 H14 N O9 P c1cc(c[n+]....
31 4KQI - NIO C6 H5 N O2 c1cc(cnc1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NIO; Similar ligands found: 5
No: Ligand ECFP6 Tc MDL keys Tc
1 NIO 1 1
2 5F8 0.487805 0.789474
3 BEZ 0.433333 0.625
4 5HN 0.428571 0.695652
5 61O 0.418605 0.714286
Ligand no: 2; Ligand: RMB; Similar ligands found: 58
No: Ligand ECFP6 Tc MDL keys Tc
1 RMB 1 1
2 PMO 0.702703 0.969231
3 RBZ 0.694444 0.969231
4 1RB 0.635135 0.984127
5 AIR 0.527027 0.855072
6 C2R 0.512821 0.808219
7 AMZ 0.512821 0.819444
8 A 0.5125 0.898551
9 AMP 0.5125 0.898551
10 7RA 0.512195 0.885714
11 71V 0.5 0.815789
12 NIA 0.5 0.75641
13 7RP 0.5 0.939394
14 IMO 0.493976 0.911765
15 P2P 0.493976 0.911765
16 PGS 0.482759 0.815789
17 AAM 0.47619 0.898551
18 G 0.465909 0.813333
19 5GP 0.465909 0.813333
20 JLN 0.458824 0.819444
21 FAI 0.458824 0.819444
22 IMP 0.443182 0.835616
23 ABM 0.44186 0.873239
24 6IA 0.44086 0.818182
25 G7M 0.438202 0.805195
26 93A 0.438202 0.743902
27 XMP 0.436782 0.824324
28 N6P 0.434343 0.925373
29 6C6 0.430108 0.837838
30 25A 0.428571 0.873239
31 ADP 0.426966 0.873239
32 A2D 0.425287 0.847222
33 B5Y 0.423077 0.826667
34 SRA 0.418605 0.849315
35 RFZ 0.417722 0.742857
36 M33 0.417582 0.861111
37 ITT 0.417582 0.898551
38 2SA 0.416667 0.837838
39 BA3 0.41573 0.847222
40 AP2 0.41573 0.837838
41 A12 0.41573 0.837838
42 IRN 0.415584 0.936508
43 RVP 0.414634 0.802817
44 6K6 0.414141 0.885714
45 HEJ 0.413043 0.873239
46 ATP 0.413043 0.873239
47 B4P 0.411111 0.847222
48 AP5 0.411111 0.847222
49 5FA 0.408602 0.873239
50 PRX 0.408602 0.849315
51 AQP 0.408602 0.873239
52 APC 0.408602 0.837838
53 GUO 0.408163 0.797297
54 AN2 0.406593 0.861111
55 AT4 0.406593 0.837838
56 AU1 0.402174 0.849315
57 CA0 0.402174 0.824324
58 ADX 0.402174 0.7625
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4KQI; Ligand: RBZ; 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: 4kqi.bio1) has 45 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4KQI; Ligand: RBZ; 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: 4kqi.bio1) has 45 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4KQI; Ligand: NIO; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4kqi.bio1) has 45 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4KQI; Ligand: NIO; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 4kqi.bio1) has 45 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback