Receptor
PDB id Resolution Class Description Source Keywords
1JHA 2 Å EC: 2.4.2.21 STRUCTURAL INVESTIGATION OF THE BIOSYNTHESIS OF ALTERNATIVE LIGANDS FOR COBAMIDES BY NICOTINATE MONONUCLEOTIDE:5,6- D IMETHYLBENZIMIDAZOLE PHOSPHORIBOSYLTRANSFERASE (COBT) FROMSA LMONELLA ENTERICA SALMONELLA ENTERICA COBT COBALAMIN BIOSYNTHESIS NN:DBI PRT N1-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
AAM A:990;
Valid;
none;
submit data
347.221 C10 H14 N5 O7 P c1nc(...
NIO A:991;
Valid;
none;
submit data
123.109 C6 H5 N O2 c1cc(...
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: AAM; Similar ligands found: 108
No: Ligand ECFP6 Tc MDL keys Tc
1 AAM 1 1
2 A 0.571429 1
3 AMP 0.571429 1
4 7RA 0.55 0.985507
5 7RP 0.5375 0.955882
6 C2R 0.532468 0.876712
7 AMZ 0.532468 0.888889
8 AIR 0.527027 0.927536
9 NIA 0.518987 0.820513
10 P2P 0.493976 0.928571
11 FAI 0.493976 0.888889
12 6MZ 0.488095 0.957143
13 71V 0.482353 0.906667
14 ADP 0.476744 0.971429
15 ABM 0.47619 0.943662
16 JLN 0.47619 0.863014
17 RMB 0.47619 0.898551
18 IMO 0.47619 0.928571
19 45A 0.47619 0.943662
20 A2D 0.47619 0.943662
21 1RB 0.47561 0.911765
22 RBZ 0.46988 0.873239
23 G 0.465909 0.905405
24 5GP 0.465909 0.905405
25 AP2 0.465116 0.931507
26 BA3 0.465116 0.943662
27 A12 0.465116 0.931507
28 ATP 0.460674 0.971429
29 HEJ 0.460674 0.971429
30 B4P 0.45977 0.943662
31 AP5 0.45977 0.943662
32 25A 0.458333 0.971429
33 APC 0.455556 0.931507
34 PRX 0.455556 0.917808
35 AQP 0.455556 0.971429
36 5FA 0.455556 0.971429
37 AT4 0.454545 0.931507
38 AN2 0.454545 0.957747
39 SRA 0.452381 0.944444
40 M33 0.449438 0.930556
41 ADX 0.449438 0.848101
42 AU1 0.449438 0.944444
43 CA0 0.449438 0.917808
44 PMO 0.448276 0.873239
45 ACP 0.444444 0.944444
46 50T 0.444444 0.957747
47 KG4 0.444444 0.917808
48 IMP 0.443182 0.90411
49 ACQ 0.44086 0.944444
50 TAT 0.44086 0.931507
51 T99 0.44086 0.931507
52 6IA 0.44086 0.858974
53 AR6 0.43956 0.943662
54 APR 0.43956 0.943662
55 93A 0.438202 0.804878
56 ADP MG 0.438202 0.942857
57 8BR 0.436782 0.931507
58 ADV 0.434783 0.905405
59 RBY 0.434783 0.905405
60 SAP 0.434783 0.918919
61 AGS 0.434783 0.918919
62 AD9 0.434783 0.944444
63 IRN 0.434211 0.867647
64 PGS 0.433333 0.857143
65 RVP 0.432099 0.847222
66 6C6 0.430108 0.905405
67 6YZ 0.427083 0.944444
68 ANP 0.425532 0.944444
69 HQG 0.42268 0.957747
70 7DD 0.422222 0.957143
71 G7M 0.422222 0.87013
72 1PR 0.421569 0.820513
73 5AL 0.421053 0.930556
74 8LE 0.421053 0.893333
75 APC MG 0.419355 0.916667
76 ADP PO3 0.419355 0.942857
77 ATP MG 0.419355 0.942857
78 A22 0.418367 0.957747
79 ITT 0.417582 0.915493
80 ATF 0.416667 0.931507
81 2SA 0.416667 0.905405
82 A3P 0.41573 0.971014
83 A2P 0.41573 0.956522
84 5SV 0.414141 0.87013
85 8LH 0.412371 0.905405
86 SRP 0.412371 0.905405
87 GAP 0.410526 0.891892
88 ADQ 0.41 0.917808
89 7DT 0.408602 0.957143
90 GUO 0.408163 0.864865
91 PTJ 0.407767 0.894737
92 SON 0.406593 0.931507
93 00A 0.405941 0.881579
94 DLL 0.405941 0.930556
95 7D5 0.404762 0.902778
96 MAP 0.40404 0.918919
97 8LQ 0.40404 0.905405
98 ADP ALF 0.402062 0.868421
99 ALF ADP 0.402062 0.868421
100 ADP BMA 0.401961 0.891892
101 6K6 0.4 0.957143
102 OOB 0.4 0.930556
103 9ZD 0.4 0.906667
104 8QN 0.4 0.930556
105 9ZA 0.4 0.906667
106 JSQ 0.4 0.918919
107 HFD 0.4 0.918919
108 OZV 0.4 0.943662
Ligand no: 2; 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
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
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