Receptor
PDB id Resolution Class Description Source Keywords
3IOC 2.5 Å EC: 6.3.2.1 CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PANTOTHENATE SYNTHETASE AT 2.50 ANG RESOLUTION IN COMPLEX WITH 5'-DEOXY-( BENZYLDISULFANYL)-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
A5D A:301;
B:302;
Valid;
Valid;
none;
none;
Kd = 210 uM
405.494 C17 H19 N5 O3 S2 c1ccc...
GOL A:701;
A:708;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
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: A5D; Similar ligands found: 176
No: Ligand ECFP6 Tc MDL keys Tc
1 A5D 1 1
2 DTA 0.746479 1
3 A6D 0.696629 0.876712
4 MTA 0.623377 0.867647
5 3DH 0.607595 0.867647
6 5N5 0.586667 0.865672
7 XYA 0.581081 0.865672
8 RAB 0.581081 0.865672
9 ADN 0.581081 0.865672
10 5CD 0.578947 0.878788
11 DSH 0.578313 0.833333
12 A4D 0.558442 0.893939
13 5X8 0.550562 0.855072
14 A7D 0.545455 0.869565
15 EP4 0.5375 0.816901
16 A 0.535714 0.808219
17 AMP 0.535714 0.808219
18 SAH 0.532609 0.857143
19 M2T 0.530864 0.819444
20 DLL 0.530612 0.8
21 SRA 0.529412 0.813333
22 AAT 0.521277 0.810811
23 FYA 0.514852 0.8
24 FA5 0.514563 0.779221
25 OOB 0.510204 0.8
26 AOC 0.505747 0.84058
27 ZAS 0.5 0.830986
28 ABM 0.5 0.786667
29 A2D 0.5 0.810811
30 J7C 0.5 0.783784
31 S8M 0.494949 0.847222
32 SON 0.494505 0.779221
33 6RE 0.494253 0.773333
34 ADX 0.48913 0.753086
35 M33 0.48913 0.776316
36 CA0 0.48913 0.766234
37 A12 0.488889 0.779221
38 AP2 0.488889 0.779221
39 BA3 0.488889 0.810811
40 AMP MG 0.488636 0.786667
41 3AM 0.488372 0.77027
42 50T 0.483871 0.776316
43 AP5 0.483516 0.810811
44 B4P 0.483516 0.810811
45 ADP 0.483516 0.786667
46 A3N 0.483146 0.828571
47 3UK 0.480392 0.789474
48 AR6 0.478723 0.786667
49 APR 0.478723 0.786667
50 AN2 0.478261 0.776316
51 S4M 0.477778 0.759494
52 GJV 0.477778 0.763158
53 5AD 0.474359 0.815385
54 RBY 0.473684 0.779221
55 ADV 0.473684 0.779221
56 AU1 0.473118 0.766234
57 A3P 0.472527 0.783784
58 MAO 0.472527 0.75
59 SXZ 0.471154 0.789474
60 ATF 0.469388 0.75641
61 ACP 0.468085 0.766234
62 SFG 0.468085 0.84058
63 ATP 0.468085 0.786667
64 5AS 0.467391 0.709302
65 SRP 0.464646 0.75641
66 PRX 0.463158 0.766234
67 AQP 0.463158 0.786667
68 5FA 0.463158 0.786667
69 APC 0.463158 0.779221
70 EEM 0.459184 0.766234
71 5AL 0.459184 0.776316
72 AD9 0.458333 0.766234
73 SA8 0.458333 0.786667
74 SAP 0.458333 0.792208
75 AGS 0.458333 0.792208
76 MHZ 0.457447 0.75
77 ADP MG 0.457447 0.776316
78 00A 0.456311 0.759494
79 NEC 0.455556 0.785714
80 G5A 0.453608 0.709302
81 SAI 0.453608 0.819444
82 BEF ADP 0.452632 0.75641
83 ADP BEF 0.452632 0.75641
84 Y3J 0.451219 0.791045
85 8QN 0.45098 0.776316
86 SMM 0.45 0.759494
87 7D7 0.45 0.808824
88 GAP 0.44898 0.766234
89 ANP 0.44898 0.766234
90 TAT 0.44898 0.802632
91 SAM 0.44898 0.789474
92 ACQ 0.44898 0.766234
93 PAJ 0.446602 0.719512
94 52H 0.445545 0.709302
95 YAP 0.444444 0.769231
96 ADP PO3 0.443299 0.808219
97 2AM 0.443182 0.76
98 AHX 0.442308 0.728395
99 53H 0.441176 0.709302
100 A5A 0.44 0.73494
101 A3G 0.43956 0.816901
102 ATP MG 0.438776 0.776316
103 OAD 0.438095 0.766234
104 25A 0.436893 0.810811
105 ADP VO4 0.435644 0.776316
106 VO4 ADP 0.435644 0.776316
107 S7M 0.435644 0.789474
108 SSA 0.435644 0.709302
109 9SN 0.435185 0.75
110 649 0.434783 0.715909
111 WAQ 0.433962 0.759494
112 PR8 0.433962 0.731707
113 AMO 0.432692 0.75641
114 4AD 0.432692 0.746835
115 7D5 0.431818 0.75
116 VMS 0.431373 0.717647
117 54H 0.431373 0.717647
118 PPS 0.43 0.731707
119 PTJ 0.429907 0.728395
120 ME8 0.429907 0.722892
121 1ZZ 0.429907 0.722892
122 3OD 0.429907 0.766234
123 OVE 0.428571 0.776316
124 PAP 0.428571 0.773333
125 TYR AMP 0.427273 0.779221
126 A22 0.427184 0.8
127 MAP 0.427184 0.746835
128 TSB 0.427184 0.72619
129 5CA 0.427184 0.709302
130 DAL AMP 0.427184 0.776316
131 KB1 0.425926 0.8
132 ADP ALF 0.425743 0.746835
133 ALF ADP 0.425743 0.746835
134 4YB 0.424779 0.712644
135 AMP DBH 0.423423 0.789474
136 GEK 0.423077 0.821918
137 5SV 0.423077 0.75
138 ANP MG 0.421569 0.746835
139 LAD 0.420561 0.740741
140 P5A 0.420561 0.696629
141 ADQ 0.419048 0.789474
142 DSZ 0.419048 0.709302
143 0UM 0.419048 0.776316
144 NSS 0.419048 0.709302
145 A1R 0.419048 0.759494
146 LSS 0.419048 0.693182
147 TXA 0.416667 0.75641
148 BIS 0.416667 0.7375
149 NB8 0.416667 0.728395
150 A3S 0.416667 0.828571
151 NVA LMS 0.415094 0.693182
152 62X 0.415094 0.7375
153 YSA 0.414414 0.729412
154 XAH 0.414414 0.722892
155 3AD 0.411765 0.850746
156 K15 0.411215 0.75641
157 LEU LMS 0.411215 0.693182
158 4UV 0.410714 0.769231
159 A2P 0.410526 0.77027
160 TYM 0.410256 0.779221
161 LAQ 0.408696 0.7875
162 A3T 0.408163 0.84058
163 A A 0.407407 0.810811
164 GSU 0.407407 0.709302
165 KAA 0.407407 0.704545
166 V3L 0.405941 0.786667
167 JB6 0.40367 0.805195
168 QQY 0.402174 0.76
169 NXX 0.401709 0.779221
170 DND 0.401709 0.779221
171 NAX 0.401709 0.731707
172 25L 0.4 0.8
173 IOT 0.4 0.697674
174 TAD 0.4 0.7625
175 D3Y 0.4 0.830986
176 MYR AMP 0.4 0.722892
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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