Receptor
PDB id Resolution Class Description Source Keywords
3IOD 1.75 Å EC: 6.3.2.1 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PANTOTHENATE SYNTHETASE AT 1.75 ANG RESOLUTION IN COMPLEX WITH 5'-DEOXY-N ITROBENZYL)DISULFANYL)-ADENOSINE MYCOBACTERIUM TUBERCULOSIS MYCOBACTERIUM TUBERCULOSIS PANTOTHENATE BIOSYNTHESIS ENZYMLIGASE INHIBITORS DRUG DESIGN FRAGMENT-BASED DYNAMIC COMBINATORIAL CHEMISTRY ATP-BINDING MAGNESIUM METAL-BINDNUCLEOTIDE-BINDING
Ref.: A FRAGMENT-BASED APPROACH TO PROBING ADENOSINE RECO SITES BY USING DYNAMIC COMBINATORIAL CHEMISTRY CHEMBIOCHEM V. 10 2772 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
A6D A:302;
B:301;
 Valid;
Valid;
 none;
none;
 Kd = 80 uM
450.492 C17 H18 N6 O5 S2 c1cc(...
EOH A:710;
A:711;
B:712;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
46.068 C2 H6 O CCO
GOL A:701;
A:708;
 Invalid;
Invalid;
 none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
SO4 A:703;
B:704;
 Invalid;
Invalid;
 none;
none;
 submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3COW 1.8 Å EC: 6.3.2.1 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PANTOTHENATE SYNTHETASE AT 1.8 ANG RESOLUTION- IN COMPLEX WITH SULPHONAMI NHIBITOR 2 MYCOBACTERIUM TUBERCULOSIS MYCOBACTERIUM TUBERCULOSIS PANTOTHENATE BIOSYNTHESIS ENZYMLIGASE INHIBITORS DRUG DESIGN ATP-BINDING MAGNESIUM MEBINDING NUCLEOTIDE-BINDING
Ref.: INHIBITION OF MYCOBACTERIUM TUBERCULOSIS PANTOTHENA SYNTHETASE BY ANALOGUES OF THE REACTION INTERMEDIAT CHEMBIOCHEM V. 9 2606 2008
Members (36)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3IVG Kd = 50 uM FG5 C20 H18 N2 O6 S COc1ccc2c(....
2 2A84 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
3 1N2O - BAL C3 H7 N O2 C(CN)C(=O)....
4 1N2E - PAF C6 H11 O4 CC(C)(CO)[....
5 3IMC Kd = 1100 uM BZ3 C9 H9 N O COc1ccc2c(....
6 4G5Y Kd = 1.69 mM 0OC C6 H9 N O2 S2 CN(C)S(=O)....
7 3IOD Kd = 80 uM A6D C17 H18 N6 O5 S2 c1cc(cc(c1....
8 3COY Kd = 0.96 uM 53H C16 H25 N7 O7 S CC(C)(C)[C....
9 3IUB Kd = 29 uM FG2 C16 H15 N3 O4 S Cc1ccc(nc1....
10 3LE8 Kd = 860 nM 2B5 C21 H18 N2 O5 COc1ccc2c(....
11 3ISJ Kd = 210 uM A8D C11 H12 N2 O4 S COc1ccc2c(....
12 2A86 - BAL C3 H7 N O2 C(CN)C(=O)....
13 3IOE Kd = 540 uM A7D C14 H21 N5 O5 S c1nc(c2c(n....
14 4G5F Kd = 0.88 mM 15N C9 H8 O4 c1ccc2c(c1....
15 4EFK Kd = 3.18 mM 0OC C6 H9 N O2 S2 CN(C)S(=O)....
16 1N2B - PAF C6 H11 O4 CC(C)(CO)[....
17 1N2G - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
18 4DDH Kd = 0.48 mM MS0 C11 H10 O4 COc1ccc2c(....
19 3COZ Kd = 2.7 uM 54H C15 H23 N7 O7 S CC(C)[C@H]....
20 1N2H - PAJ C16 H24 N5 O10 P CC(C)(CO)[....
21 3COW Kd = 0.125 uM 52H C16 H24 N6 O8 S CC(C)(C)[C....
22 3IOC Kd = 210 uM A5D C17 H19 N5 O3 S2 c1ccc(cc1)....
23 3IVC Kd = 76 uM FG4 C21 H17 N O6 COc1ccc2c(....
24 4EF6 Kd = 1.18 mM I2E C10 H10 O4 c1cc2c(cc1....
25 4DDK Kd = 5.13 mM 0HN C8 H6 O4 c1cc2c(cc1....
26 3IMG - BZ3 C9 H9 N O COc1ccc2c(....
27 4FZJ Kd = 0.74 mM 0W1 C8 H8 N2 O2 S Cc1c2cc(sc....
28 1N2I - PAJ C16 H24 N5 O10 P CC(C)(CO)[....
29 3IUE Kd = 1.5 uM FG3 C18 H17 N3 O6 S Cc1ccc(nc1....
30 3IVX Kd = 1.8 uM FG6 C20 H16 N2 O7 S COc1ccc2c(....
31 2A7X - AMP C10 H14 N5 O7 P c1nc(c2c(n....
32 4DE5 Kd = 0.67 mM 0JD C9 H8 O4 c1ccc2c(c1....
33 1N2J - PAF C6 H11 O4 CC(C)(CO)[....
34 3IME Kd = 1000 uM BZ2 C9 H6 O3 c1ccc2c(c1....
35 4DDM Kd = 3.48 mM 0HO C7 H4 N2 O2 S c1cc2c(cc1....
36 3IOB Kd = 380 uM A4D C10 H13 N5 O3 S c1nc(c2c(n....
70% Homology Family (36)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3IVG Kd = 50 uM FG5 C20 H18 N2 O6 S COc1ccc2c(....
2 2A84 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
3 1N2O - BAL C3 H7 N O2 C(CN)C(=O)....
4 1N2E - PAF C6 H11 O4 CC(C)(CO)[....
5 3IMC Kd = 1100 uM BZ3 C9 H9 N O COc1ccc2c(....
6 4G5Y Kd = 1.69 mM 0OC C6 H9 N O2 S2 CN(C)S(=O)....
7 3IOD Kd = 80 uM A6D C17 H18 N6 O5 S2 c1cc(cc(c1....
8 3COY Kd = 0.96 uM 53H C16 H25 N7 O7 S CC(C)(C)[C....
9 3IUB Kd = 29 uM FG2 C16 H15 N3 O4 S Cc1ccc(nc1....
10 3LE8 Kd = 860 nM 2B5 C21 H18 N2 O5 COc1ccc2c(....
11 3ISJ Kd = 210 uM A8D C11 H12 N2 O4 S COc1ccc2c(....
12 2A86 - BAL C3 H7 N O2 C(CN)C(=O)....
13 3IOE Kd = 540 uM A7D C14 H21 N5 O5 S c1nc(c2c(n....
14 4G5F Kd = 0.88 mM 15N C9 H8 O4 c1ccc2c(c1....
15 4EFK Kd = 3.18 mM 0OC C6 H9 N O2 S2 CN(C)S(=O)....
16 1N2B - PAF C6 H11 O4 CC(C)(CO)[....
17 1N2G - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
18 4DDH Kd = 0.48 mM MS0 C11 H10 O4 COc1ccc2c(....
19 3COZ Kd = 2.7 uM 54H C15 H23 N7 O7 S CC(C)[C@H]....
20 1N2H - PAJ C16 H24 N5 O10 P CC(C)(CO)[....
21 3COW Kd = 0.125 uM 52H C16 H24 N6 O8 S CC(C)(C)[C....
22 3IOC Kd = 210 uM A5D C17 H19 N5 O3 S2 c1ccc(cc1)....
23 3IVC Kd = 76 uM FG4 C21 H17 N O6 COc1ccc2c(....
24 4EF6 Kd = 1.18 mM I2E C10 H10 O4 c1cc2c(cc1....
25 4DDK Kd = 5.13 mM 0HN C8 H6 O4 c1cc2c(cc1....
26 3IMG - BZ3 C9 H9 N O COc1ccc2c(....
27 4FZJ Kd = 0.74 mM 0W1 C8 H8 N2 O2 S Cc1c2cc(sc....
28 1N2I - PAJ C16 H24 N5 O10 P CC(C)(CO)[....
29 3IUE Kd = 1.5 uM FG3 C18 H17 N3 O6 S Cc1ccc(nc1....
30 3IVX Kd = 1.8 uM FG6 C20 H16 N2 O7 S COc1ccc2c(....
31 2A7X - AMP C10 H14 N5 O7 P c1nc(c2c(n....
32 4DE5 Kd = 0.67 mM 0JD C9 H8 O4 c1ccc2c(c1....
33 1N2J - PAF C6 H11 O4 CC(C)(CO)[....
34 3IME Kd = 1000 uM BZ2 C9 H6 O3 c1ccc2c(c1....
35 4DDM Kd = 3.48 mM 0HO C7 H4 N2 O2 S c1cc2c(cc1....
36 3IOB Kd = 380 uM A4D C10 H13 N5 O3 S c1nc(c2c(n....
50% Homology Family (36)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3IVG Kd = 50 uM FG5 C20 H18 N2 O6 S COc1ccc2c(....
2 2A84 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
3 1N2O - BAL C3 H7 N O2 C(CN)C(=O)....
4 1N2E - PAF C6 H11 O4 CC(C)(CO)[....
5 3IMC Kd = 1100 uM BZ3 C9 H9 N O COc1ccc2c(....
6 4G5Y Kd = 1.69 mM 0OC C6 H9 N O2 S2 CN(C)S(=O)....
7 3IOD Kd = 80 uM A6D C17 H18 N6 O5 S2 c1cc(cc(c1....
8 3COY Kd = 0.96 uM 53H C16 H25 N7 O7 S CC(C)(C)[C....
9 3IUB Kd = 29 uM FG2 C16 H15 N3 O4 S Cc1ccc(nc1....
10 3LE8 Kd = 860 nM 2B5 C21 H18 N2 O5 COc1ccc2c(....
11 3ISJ Kd = 210 uM A8D C11 H12 N2 O4 S COc1ccc2c(....
12 2A86 - BAL C3 H7 N O2 C(CN)C(=O)....
13 3IOE Kd = 540 uM A7D C14 H21 N5 O5 S c1nc(c2c(n....
14 4G5F Kd = 0.88 mM 15N C9 H8 O4 c1ccc2c(c1....
15 4EFK Kd = 3.18 mM 0OC C6 H9 N O2 S2 CN(C)S(=O)....
16 1N2B - PAF C6 H11 O4 CC(C)(CO)[....
17 1N2G - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
18 4DDH Kd = 0.48 mM MS0 C11 H10 O4 COc1ccc2c(....
19 3COZ Kd = 2.7 uM 54H C15 H23 N7 O7 S CC(C)[C@H]....
20 1N2H - PAJ C16 H24 N5 O10 P CC(C)(CO)[....
21 3COW Kd = 0.125 uM 52H C16 H24 N6 O8 S CC(C)(C)[C....
22 3IOC Kd = 210 uM A5D C17 H19 N5 O3 S2 c1ccc(cc1)....
23 3IVC Kd = 76 uM FG4 C21 H17 N O6 COc1ccc2c(....
24 4EF6 Kd = 1.18 mM I2E C10 H10 O4 c1cc2c(cc1....
25 4DDK Kd = 5.13 mM 0HN C8 H6 O4 c1cc2c(cc1....
26 3IMG - BZ3 C9 H9 N O COc1ccc2c(....
27 4FZJ Kd = 0.74 mM 0W1 C8 H8 N2 O2 S Cc1c2cc(sc....
28 1N2I - PAJ C16 H24 N5 O10 P CC(C)(CO)[....
29 3IUE Kd = 1.5 uM FG3 C18 H17 N3 O6 S Cc1ccc(nc1....
30 3IVX Kd = 1.8 uM FG6 C20 H16 N2 O7 S COc1ccc2c(....
31 2A7X - AMP C10 H14 N5 O7 P c1nc(c2c(n....
32 4DE5 Kd = 0.67 mM 0JD C9 H8 O4 c1ccc2c(c1....
33 1N2J - PAF C6 H11 O4 CC(C)(CO)[....
34 3IME Kd = 1000 uM BZ2 C9 H6 O3 c1ccc2c(c1....
35 4DDM Kd = 3.48 mM 0HO C7 H4 N2 O2 S c1cc2c(cc1....
36 3IOB Kd = 380 uM A4D C10 H13 N5 O3 S c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: A6D; Similar ligands found: 131
No: Ligand ECFP6 Tc MDL keys Tc
1 A6D 1 1
2 A5D 0.696629 0.876712
3 DTA 0.646341 0.876712
4 MTA 0.545455 0.766234
5 3DH 0.533333 0.766234
6 5N5 0.511628 0.763158
7 DSH 0.510638 0.740741
8 ADN 0.505882 0.763158
9 XYA 0.505882 0.763158
10 RAB 0.505882 0.763158
11 5CD 0.505747 0.773333
12 5X8 0.50505 0.75641
13 SAH 0.490196 0.759494
14 A 0.489362 0.740741
15 AMP 0.489362 0.740741
16 A4D 0.488636 0.786667
17 A7D 0.484848 0.769231
18 EP4 0.472527 0.725
19 SRA 0.46875 0.746988
20 M2T 0.467391 0.75
21 AMP MG 0.463918 0.743902
22 ATF 0.462264 0.697674
23 50T 0.460784 0.714286
24 ADP 0.46 0.722892
25 A2D 0.459184 0.743902
26 ABM 0.459184 0.722892
27 SON 0.455446 0.717647
28 GJV 0.454545 0.722892
29 6RE 0.453608 0.731707
30 AAT 0.45283 0.722892
31 M33 0.45098 0.714286
32 CA0 0.45098 0.705882
33 ADX 0.45098 0.696629
34 BA3 0.45 0.743902
35 AP2 0.45 0.717647
36 A12 0.45 0.717647
37 AOC 0.44898 0.74359
38 3UK 0.446429 0.72619
39 AP5 0.445545 0.743902
40 B4P 0.445545 0.743902
41 OOB 0.445455 0.73494
42 J7C 0.444444 0.719512
43 ZAS 0.443299 0.828947
44 AN2 0.441176 0.73494
45 S4M 0.44 0.701149
46 SXZ 0.438596 0.705882
47 DLL 0.4375 0.73494
48 ADP MG 0.436893 0.73494
49 AU1 0.436893 0.746988
50 A3P 0.435644 0.719512
51 SAI 0.433962 0.728395
52 3AM 0.43299 0.707317
53 ADP BEF 0.432692 0.717647
54 BEF ADP 0.432692 0.717647
55 ACP 0.432692 0.705882
56 SFG 0.432692 0.74359
57 ATP 0.432692 0.722892
58 S8M 0.432432 0.797468
59 5AS 0.431373 0.677419
60 SRP 0.431193 0.697674
61 SMM 0.431193 0.701149
62 A3N 0.43 0.734177
63 GAP 0.429907 0.72619
64 SAM 0.429907 0.72619
65 PR8 0.429825 0.677778
66 PRX 0.428571 0.705882
67 AQP 0.428571 0.722892
68 PAJ 0.428571 0.666667
69 APC 0.428571 0.717647
70 5FA 0.428571 0.722892
71 APR 0.428571 0.722892
72 AR6 0.428571 0.722892
73 5AL 0.425926 0.714286
74 EEM 0.425926 0.705882
75 00A 0.424779 0.701149
76 RBY 0.424528 0.717647
77 AGS 0.424528 0.729412
78 ADP PO3 0.424528 0.7625
79 ADV 0.424528 0.717647
80 SAP 0.424528 0.729412
81 AD9 0.424528 0.705882
82 SA8 0.424528 0.702381
83 MAO 0.421569 0.752941
84 G5A 0.420561 0.677419
85 ATP MG 0.420561 0.73494
86 8QN 0.419643 0.714286
87 9SN 0.418803 0.693182
88 VO4 ADP 0.418182 0.73494
89 ADP VO4 0.418182 0.73494
90 P5A 0.417391 0.666667
91 ANP 0.416667 0.746988
92 TAT 0.416667 0.738095
93 ACQ 0.416667 0.705882
94 5AD 0.41573 0.716216
95 FA5 0.415254 0.717647
96 52H 0.414414 0.677419
97 3OD 0.413793 0.705882
98 FYA 0.413793 0.73494
99 AHX 0.412281 0.732558
100 TYR AMP 0.411765 0.738095
101 PAP 0.411215 0.710843
102 DAL AMP 0.410714 0.73494
103 53H 0.410714 0.677419
104 MHZ 0.409524 0.693182
105 A5A 0.409091 0.7
106 ALF ADP 0.409091 0.709302
107 ADP ALF 0.409091 0.709302
108 2AM 0.408163 0.698795
109 25A 0.40708 0.743902
110 GEK 0.40708 0.753086
111 A3G 0.405941 0.725
112 NEC 0.405941 0.696203
113 S7M 0.405405 0.72619
114 SSA 0.405405 0.677419
115 ANP MG 0.405405 0.75
116 A A 0.405172 0.765432
117 WAQ 0.405172 0.701149
118 ADQ 0.403509 0.72619
119 AMO 0.403509 0.697674
120 4AD 0.403509 0.709302
121 LSS 0.403509 0.663158
122 YAP 0.403361 0.709302
123 VMS 0.401786 0.684783
124 54H 0.401786 0.684783
125 BIS 0.401709 0.681818
126 PTJ 0.401709 0.674157
127 1ZZ 0.401709 0.67033
128 ME8 0.401709 0.67033
129 PPS 0.4 0.677778
130 A3S 0.4 0.734177
131 NVA LMS 0.4 0.680851
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3COW; Ligand: 52H; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3cow.bio1) has 42 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3COW; Ligand: 52H; Similar sites found: 28
This union binding pocket(no: 2) in the query (biounit: 3cow.bio1) has 45 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3JRX S1A 0.03478 0.40027 1.66113
2 3ZIU LSS 0.00000576 0.41197 1.99336
3 2PID YSA 0.00001517 0.41256 2.24719
4 1PFY MSP 0.000009007 0.41365 2.32558
5 2YLN CYS 0.03763 0.41859 3.18021
6 3C8Z 5CA 0.00001508 0.55124 3.32226
7 4E2J MOF 0.01038 0.41359 3.6
8 5UFS 1TA 0.02043 0.40034 3.62903
9 1G27 BB1 0.0266 0.40308 4.16667
10 4GQY AMP 0.02535 0.42033 4.24242
11 3R9V DXC 0.002825 0.42978 4.31894
12 1R6T TYM 0.0001066 0.4568 4.65116
13 4J75 TYM 0.000005874 0.43172 4.88998
14 4IZY 1J2 0.02476 0.40178 5.31561
15 1R4W GSH 0.03057 0.41247 5.75221
16 2QTR NXX 0.0001706 0.407 5.82011
17 1S9D AFB 0.03721 0.41143 6.40394
18 2X1L ADN 0.00006608 0.5435 6.97674
19 3ND6 ATP 0.0001626 0.40209 7.30897
20 3HUN ZZ7 0.03785 0.41468 8.30565
21 2XG5 EC5 0.01024 0.45217 8.7156
22 2XG5 EC2 0.01024 0.45217 8.7156
23 5BXV MGP 0.02564 0.42693 9.09091
24 3KFL ME8 0.0000005149 0.44981 9.63455
25 1WS1 BB2 0.03719 0.40174 12.8205
26 3KP6 SAL 0.008535 0.45594 13.245
27 3HL4 CDC 0.001182 0.46333 14.4068
28 1N1D C2G 0.003558 0.42834 17.0543
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