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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: 96
No: Ligand ECFP6 Tc MDL keys Tc
1 AAM 1 1
2 AMP 0.571429 1
3 A 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 FAI 0.493976 0.888889
11 P2P 0.493976 0.928571
12 71V 0.482353 0.906667
13 ADP 0.476744 0.971429
14 JLN 0.47619 0.863014
15 RMB 0.47619 0.898551
16 A2D 0.47619 0.943662
17 ABM 0.47619 0.943662
18 IMO 0.47619 0.928571
19 1RB 0.47561 0.911765
20 RBZ 0.46988 0.873239
21 G 0.465909 0.905405
22 5GP 0.465909 0.905405
23 BA3 0.465116 0.943662
24 A12 0.465116 0.931507
25 AP2 0.465116 0.931507
26 HEJ 0.460674 0.971429
27 ATP 0.460674 0.971429
28 AP5 0.45977 0.943662
29 B4P 0.45977 0.943662
30 25A 0.458333 0.971429
31 APC 0.455556 0.931507
32 5FA 0.455556 0.971429
33 AQP 0.455556 0.971429
34 PRX 0.455556 0.917808
35 AT4 0.454545 0.931507
36 AN2 0.454545 0.957747
37 SRA 0.452381 0.944444
38 AU1 0.449438 0.944444
39 ADX 0.449438 0.848101
40 CA0 0.449438 0.917808
41 M33 0.449438 0.930556
42 PMO 0.448276 0.873239
43 50T 0.444444 0.957747
44 ACP 0.444444 0.944444
45 IMP 0.443182 0.90411
46 6IA 0.44086 0.858974
47 TAT 0.44086 0.931507
48 T99 0.44086 0.931507
49 ACQ 0.44086 0.944444
50 APR 0.43956 0.943662
51 AR6 0.43956 0.943662
52 93A 0.438202 0.804878
53 8BR 0.436782 0.931507
54 RBY 0.434783 0.905405
55 AGS 0.434783 0.918919
56 SAP 0.434783 0.918919
57 ADV 0.434783 0.905405
58 AD9 0.434783 0.944444
59 IRN 0.434211 0.867647
60 PGS 0.433333 0.857143
61 RVP 0.432099 0.847222
62 6C6 0.430108 0.905405
63 6YZ 0.427083 0.944444
64 ANP 0.425532 0.944444
65 7DD 0.422222 0.957143
66 G7M 0.422222 0.87013
67 1PR 0.421569 0.820513
68 5AL 0.421053 0.930556
69 ADP PO3 0.419355 0.942857
70 A22 0.418367 0.957747
71 ITT 0.417582 0.915493
72 2SA 0.416667 0.905405
73 ATF 0.416667 0.931507
74 A2P 0.41573 0.956522
75 A3P 0.41573 0.971014
76 5SV 0.414141 0.87013
77 SRP 0.412371 0.905405
78 GAP 0.410526 0.891892
79 ADQ 0.41 0.917808
80 7DT 0.408602 0.957143
81 GUO 0.408163 0.864865
82 PTJ 0.407767 0.894737
83 SON 0.406593 0.931507
84 00A 0.405941 0.881579
85 DLL 0.405941 0.930556
86 7D5 0.404762 0.902778
87 MAP 0.40404 0.918919
88 ADP ALF 0.402062 0.868421
89 ALF ADP 0.402062 0.868421
90 ADP BMA 0.401961 0.891892
91 6K6 0.4 0.957143
92 8QN 0.4 0.930556
93 HFD 0.4 0.918919
94 9ZA 0.4 0.906667
95 OOB 0.4 0.930556
96 9ZD 0.4 0.906667
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: 91
This union binding pocket(no: 1) in the query (biounit: 4kqi.bio1) has 45 residues
No: Leader PDB Ligand Sequence Similarity
1 4LIK CIT None
2 5H4S RAM 1.05634
3 2BO4 FLC 1.40449
4 3LRE ADP 1.40845
5 1B4N GUA 1.68539
6 1RZM E4P 1.77515
7 1V7Z CRN 1.92308
8 2FYF PLP 1.96629
9 5GJO PLP 1.96629
10 4PPF FLC 2
11 4KVL PLM 2.24719
12 5VJE GOS 2.24719
13 5L3S G 2.34899
14 3ITJ CIT 2.36686
15 4LH7 1X8 2.47678
16 3V2U GLA 2.52809
17 3HQ9 OXL 2.6087
18 1JJ7 ADP 2.69231
19 1H5R THM 2.73038
20 1H5T TYD 2.73038
21 4B2D FBP 2.73723
22 1BG2 ADP 2.76923
23 2B7N NTM 2.9304
24 5E5U MLI 3.01508
25 5F1V 3VN 3.0303
26 2C3H GLC GLC 3.06122
27 1IIM TTP 3.08219
28 5FPE 3TR 3.08989
29 1WDN GLN 3.09735
30 4DFU QUE 3.10559
31 1XPJ TLA 3.1746
32 1TZD ADP 3.27273
33 6CWH 6LA 3.2967
34 1JTQ LY3 3.40909
35 2J0W ASP 3.56347
36 3UN3 G16 3.65169
37 4XFR CIT 3.65169
38 2VVG ADP 3.71429
39 5O6Y 5YA 3.73832
40 2VWT PYR 3.74532
41 6C0B MLI 3.84615
42 1EQ2 ADQ 3.87097
43 1H70 CIR 3.92157
44 2AWN ADP 3.93258
45 4MN7 SME 4.02685
46 1LVW TYD 4.0678
47 1M0S CIT 4.10959
48 6AM8 TRP 4.21348
49 3LE7 ADE 4.21456
50 4O48 ASP 4.21687
51 1T5C ADP 4.29799
52 4WEI GLC GAL 4.33213
53 4WZ6 ATP 4.48276
54 5CGE 51F 4.69314
55 5HWK BEZ 5
56 1KYZ FER 5.05618
57 1G6H ADP 5.05837
58 3JQM GTP 5.09554
59 1LK7 DER 5.24017
60 5FBK TCR 5.33708
61 1VBO MAN 5.36913
62 2WCU FUC 5.36913
63 2FJK 13P 5.57377
64 2D2F ADP 5.6
65 3KIF GDL 5.66038
66 2PZE ATP 5.67686
67 3AB4 THR 5.70071
68 3AB4 LYS 5.70071
69 1TKU 5RP 5.88235
70 5GMH RX8 5.89888
71 1UPF URF 6.25
72 2B99 RDL 6.41026
73 5N6N SUC 6.46067
74 3C56 PH4 6.51466
75 3HQP FDP 6.74157
76 3GAY P6T 6.81115
77 2Y65 ADP 7.02247
78 1ITW ICT 7.30337
79 1BKC INN 7.42188
80 1P4V GLY 7.45763
81 1H5S TMP 7.50853
82 4RKX 3S9 7.58427
83 2CBZ ATP 8.01688
84 1RL4 BL5 8.51064
85 1PIE GLA 9.83146
86 2DT9 THR 10.1796
87 2KIN ADP 10.5042
88 2XCM ADP 10.8696
89 1S68 AMP 12.0482
90 5B2E MQG 13.6029
91 3Q8U ADP 22.293
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: 71
This union binding pocket(no: 3) in the query (biounit: 4kqi.bio1) has 45 residues
No: Leader PDB Ligand Sequence Similarity
1 4LIK CIT None
2 5H4S RAM 1.05634
3 2BO4 FLC 1.40449
4 3LRE ADP 1.40845
5 1RZM E4P 1.77515
6 1V7Z CRN 1.92308
7 2FYF PLP 1.96629
8 4PPF FLC 2
9 4KVL PLM 2.24719
10 5VJE GOS 2.24719
11 5L3S G 2.34899
12 3ITJ CIT 2.36686
13 1RRC ADP 2.65781
14 1H5R THM 2.73038
15 1H5T TYD 2.73038
16 1BG2 ADP 2.76923
17 1JJV ATP 2.91262
18 5E5U MLI 3.01508
19 5F1V 3VN 3.0303
20 2C3H GLC GLC 3.06122
21 1IIM TTP 3.08219
22 5FPE 3TR 3.08989
23 1ZGS XMM 3.08989
24 1WDN GLN 3.09735
25 1XPJ TLA 3.1746
26 1TZD ADP 3.27273
27 6CWH 6LA 3.2967
28 2J0W ASP 3.56347
29 3UN3 G16 3.65169
30 4XFR CIT 3.65169
31 2VVG ADP 3.71429
32 5O6Y 5YA 3.73832
33 2VWT PYR 3.74532
34 6C0B MLI 3.84615
35 1EQ2 ADQ 3.87097
36 1H70 CIR 3.92157
37 2AWN ADP 3.93258
38 4MN7 SME 4.02685
39 1LVW TYD 4.0678
40 3LE7 ADE 4.21456
41 4O48 ASP 4.21687
42 4WEI GLC GAL 4.33213
43 1LDN FBP 4.43038
44 4WZ6 ATP 4.48276
45 5HWK BEZ 5
46 3JQM GTP 5.09554
47 5FBK TCR 5.33708
48 1XVB BHL 5.33708
49 1VBO MAN 5.36913
50 2WCU FUC 5.36913
51 2FJK 13P 5.57377
52 2PZE ATP 5.67686
53 3AB4 THR 5.70071
54 3AB4 LYS 5.70071
55 1TKU 5RP 5.88235
56 5GMH RX8 5.89888
57 1UPF URF 6.25
58 2B99 RDL 6.41026
59 5N6N SUC 6.46067
60 3N9R TD3 6.51466
61 3C56 PH4 6.51466
62 2Y65 ADP 7.02247
63 1P4V GLY 7.45763
64 1H5S TMP 7.50853
65 4RKX 3S9 7.58427
66 2CBZ ATP 8.01688
67 2DT9 THR 10.1796
68 1O5O U5P 10.4072
69 4B5W PYR 12.5
70 5B2E MQG 13.6029
71 1APZ ASP 25.9259
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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