-->
Receptor
PDB id Resolution Class Description Source Keywords
5ESO 2.05 Å EC: 2.2.1.9 CRYSTAL STRUCTURE OF M. TUBERCULOSIS MEND WITH THDP, MG2+ AN ISOCHORISMATE BOUND MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCH37RV) MENAQUINONE BIOSYNTHESIS MEND 2-SUCCINYL-5-ENOLPYRUVYL-6-HCYCLOHEXADIENE-1-CARBOXYLATE SYNTHASE THIAMIN-DIPHOSPHATE ENZYME PYRUVATE OXIDASE FAMILY TRANSFERASE
Ref.: STRUCTURAL VIEWS ALONG THE MYCOBACTERIUM TUBERCULOS REACTION PATHWAY ILLUMINATE KEY ASPECTS OF THIAMIN DIPHOSPHATE-DEPENDENT ENZYME MECHANISMS. STRUCTURE V. 24 1167 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BME D:603;
C:606;
Invalid;
Invalid;
none;
none;
submit data
78.133 C2 H6 O S C(CS)...
ISC B:602;
A:602;
Valid;
Valid;
none;
none;
submit data
226.183 C10 H10 O6 C=C(C...
MG B:601;
D:601;
A:601;
C:601;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
FMT C:604;
C:603;
A:603;
B:603;
B:604;
C:602;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
46.025 C H2 O2 C(=O)...
GOL B:605;
A:604;
A:605;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
TDP D:602;
C:605;
Valid;
Valid;
none;
none;
submit data
424.306 C12 H18 N4 O7 P2 S Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5ESO 2.05 Å EC: 2.2.1.9 CRYSTAL STRUCTURE OF M. TUBERCULOSIS MEND WITH THDP, MG2+ AN ISOCHORISMATE BOUND MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCH37RV) MENAQUINONE BIOSYNTHESIS MEND 2-SUCCINYL-5-ENOLPYRUVYL-6-HCYCLOHEXADIENE-1-CARBOXYLATE SYNTHASE THIAMIN-DIPHOSPHATE ENZYME PYRUVATE OXIDASE FAMILY TRANSFERASE
Ref.: STRUCTURAL VIEWS ALONG THE MYCOBACTERIUM TUBERCULOS REACTION PATHWAY ILLUMINATE KEY ASPECTS OF THIAMIN DIPHOSPHATE-DEPENDENT ENZYME MECHANISMS. STRUCTURE V. 24 1167 2016
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5ESU - TOI C26 H35 N4 O16 P2 S [H]/N=C/1C....
2 5ESS - TOG C16 H24 N4 O10 P2 S Cc1c(sc([n....
3 5ESO - ISC C10 H10 O6 C=C(C(=O)O....
4 5ESD - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5ESU - TOI C26 H35 N4 O16 P2 S [H]/N=C/1C....
2 5ESS - TOG C16 H24 N4 O10 P2 S Cc1c(sc([n....
3 5ESO - ISC C10 H10 O6 C=C(C(=O)O....
4 5ESD - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5ESU - TOI C26 H35 N4 O16 P2 S [H]/N=C/1C....
2 5ESS - TOG C16 H24 N4 O10 P2 S Cc1c(sc([n....
3 5ESO - ISC C10 H10 O6 C=C(C(=O)O....
4 5ESD - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ISC; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 ISC 1 1
2 QLI 0.55102 0.714286
Ligand no: 2; Ligand: TDP; Similar ligands found: 33
No: Ligand ECFP6 Tc MDL keys Tc
1 TDP 1 1
2 TPP 0.84 0.985714
3 V4E 0.797468 0.985714
4 TPS 0.77027 0.942857
5 TMV 0.75 0.944444
6 VNP 0.703704 0.945205
7 N1T 0.674699 1
8 2TP 0.609195 0.918919
9 VIB 0.605263 0.760563
10 5SR 0.582418 0.958333
11 FTP 0.574713 0.847222
12 O2T 0.546392 0.896104
13 PYI 0.483871 0.873239
14 HTL 0.474227 0.945205
15 TDW 0.474227 0.958333
16 AUJ 0.47 0.907895
17 THV 0.46 0.945205
18 TD6 0.457143 0.907895
19 WWF 0.455446 0.92
20 TOG 0.451923 0.907895
21 TPW 0.451613 0.885714
22 THY 0.45098 0.932432
23 TD8 0.448598 0.907895
24 TD9 0.448598 0.907895
25 THW 0.447619 0.945205
26 TDL 0.446602 0.884615
27 TDK 0.442308 0.907895
28 D7K 0.415929 0.896104
29 TPU 0.410526 0.828947
30 R1T 0.405941 0.873239
31 S1T 0.405941 0.873239
32 T5X 0.403509 0.884615
33 T6F 0.403509 0.884615
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5ESO; Ligand: ISC; Similar sites found with APoc: 197
This union binding pocket(no: 1) in the query (biounit: 5eso.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
1 4A59 AMP 1.21951
2 1ZPD DPX 1.23239
3 3AJM 4IP 1.87793
4 2C42 TPP 1.91638
5 2C42 PYR 1.91638
6 4KVL PLM 1.91638
7 4YJ1 ADP 1.91638
8 1TKB N1T 2.09059
9 5EGH PC 2.0979
10 1NLM UD1 2.1978
11 1TE2 PGA 2.21239
12 1R9J TPP 2.26481
13 1KRH FAD 2.36686
14 1J78 OLA 2.40175
15 5B48 TDN 2.43902
16 1R2J FAD 2.45902
17 2DE4 BPS 2.46575
18 5N6N SUC 2.5
19 9ABP GLA 2.61438
20 9ABP GAL 2.61438
21 4YDS ATP 2.63158
22 4CCW VKC 2.67559
23 3I7S PYR 2.73973
24 4D5G FAD 2.78746
25 4D5G TPP 2.78746
26 5ND5 TPP 2.78746
27 3AI7 TPP 2.78746
28 5TBS ADE 2.78746
29 3OBK PBG 2.80899
30 1PFK ADP 2.8125
31 1GDE GLU PLP 2.82776
32 5W3Y ACO 2.84091
33 5CGE 51F 2.88809
34 4NTO 1PW 2.89855
35 1RJW ETF 2.94985
36 3IHB GLU 2.96167
37 1KAR HSM 2.99539
38 3U7Q HCA 3.04878
39 3BRE C2E 3.07263
40 3W9F I3P 3.07692
41 2OG7 AHB 3.08123
42 2O1S TDP 3.13589
43 1ITZ TPP 3.13589
44 2IYA UDP 3.13589
45 1D8C GLV 3.13589
46 4G05 JZ3 3.15457
47 4G86 BNT 3.16901
48 5G1N PAL 3.18471
49 3LL5 IP8 3.21285
50 3IT7 TLA 3.2967
51 3B8I OXL 3.3101
52 2VK4 TPP 3.37478
53 5NM7 GLY 3.38346
54 4PPF FLC 3.42857
55 4WZ6 ATP 3.44828
56 3WW2 SF9 3.51562
57 3MMH SME 3.59281
58 4WJT NAG 3.59281
59 1U3G ADP 3.7037
60 3B5J 12D 3.7037
61 1QPB PYM 3.73002
62 1QPB TPP 3.73002
63 4NV0 MG7 3.76176
64 4JZ8 CIT 3.78549
65 5B47 PYR 3.83275
66 5B47 TPP 3.83275
67 2YIC TPP 3.83275
68 5OKU 0L1 3.89222
69 3A51 VDY 3.89294
70 2Q8M AMP 3.91566
71 2BOY BHO 3.93701
72 3FJG 3PG 3.98406
73 2CE7 ADP 4.00697
74 2NSX IFM 4.00697
75 1RP7 TZD 4.00697
76 1UMD TDP COI 4.01235
77 2OZL TPP 4.10557
78 3S2U UD1 4.10959
79 5C9P FUC 4.19948
80 1BW9 PPY 4.21348
81 1OHE ACE ALA SEP PRO 4.31034
82 4AVV GHE 4.41176
83 4AVV CD 4.41176
84 4HE2 AMP 4.43787
85 3KC1 2T6 4.45104
86 2B99 RDL 4.48718
87 2O1C PPV 4.66667
88 1V5F TPP 4.70383
89 1V5F FAD 4.70383
90 1EJH M7G 4.73684
91 2QV7 ADP 4.74777
92 6CEP OXM 4.79042
93 5A96 GTP 4.81928
94 4OFG PCG 4.86111
95 6MFL OPV 4.87013
96 2J5V PCA 4.90463
97 2Q8G AZX 4.914
98 3KO0 TFP 4.9505
99 1T36 ORN 4.97382
100 4K79 GAL A2G 5
101 1W6F ISZ 5.03597
102 2FV1 GAD NDG 5.03979
103 2P3V SRT 5.07812
104 2C3H GLC GLC 5.10204
105 5AGR A52 5.17241
106 3NFD COA 5.22876
107 2JAP J01 5.26316
108 3EGI ADP 5.33981
109 4JCA CIT 5.38922
110 4R5Z PMP 5.44959
111 2UZH CDP 5.45455
112 1NXJ TLA 5.46448
113 1RRV TYD 5.52885
114 5KL0 G16 5.56745
115 3LTW HLZ 5.57491
116 5C8W PCG 5.59441
117 1G2O IMH 5.59701
118 3SHR CMP 5.68562
119 3DVA TPW 5.69106
120 1XVB 3BR 5.6926
121 3H4T UDP 5.69307
122 1W85 TDP 5.70652
123 4KGD TDP 5.74913
124 4KGD FAD 5.74913
125 2R0D 4IP 5.76369
126 2R09 4IP 5.76369
127 2J0W ASP 5.79065
128 3EYA TDP 6.01093
129 1LES GLC FRU 6.07735
130 6CZY PMP 6.07735
131 5URY PAM 6.16438
132 2Q28 TPP 6.20567
133 2ACV UDP 6.2635
134 5VEQ PMP 6.56934
135 6FBA D48 6.59026
136 2C31 TZD 6.69014
137 2C31 ADP 6.69014
138 4R78 AMP 6.79612
139 3ITJ CIT 6.80473
140 3EXH TPP 6.80628
141 4WBD CIT 6.83919
142 2A5F NAD 7.42857
143 3FSJ D7K 7.57576
144 4UEC MGT 7.69231
145 2BO4 FLC 7.80856
146 5T48 MGP 7.8125
147 2VBF TPP 8.24561
148 3NOJ PYR 8.40336
149 3IAE D7K 8.53659
150 6G47 SIA SIA 8.61244
151 2OG2 MLI 8.6351
152 2UZ1 TPP 8.70337
153 2IHT TPP 8.726
154 1UPA TPP 8.726
155 2W97 MGO 8.75576
156 4HSE ADP 8.81612
157 1H5R THM 8.87372
158 2IHU TP9 8.90052
159 3X27 TRP 8.95522
160 4YEF 4CQ 8.98876
161 1H5S TMP 9.21502
162 1Z0N BCD 9.375
163 5EXE 5SR 9.52381
164 5AHW CMP 9.52381
165 1YBH P22 9.58188
166 2PZE ATP 9.60699
167 2O66 FLC 9.62963
168 4QS9 BGC 9.70464
169 4UDK BMA 9.79827
170 1YQT ADP 9.8513
171 1OZH HE3 9.93031
172 5T46 MGP 10.6061
173 1WAP TRP 10.6667
174 1JJ7 ADP 10.7692
175 4RJK TPP 11.3835
176 4RJK TDL 11.3835
177 2AWN ADP 12.0735
178 4JNJ BTN 12.1739
179 5E5U MLI 12.5628
180 5FII PHE 12.7451
181 1LVW TYD 12.8814
182 1T0S BML 13.9535
183 5WKC TP9 14.1115
184 5WKC AUJ 14.1115
185 1T9D P25 14.1115
186 1T9D FAD 14.1115
187 1T9D 1MM 14.1115
188 1T9D P22 14.1115
189 1T9D PYD 14.1115
190 5ABX MGP 14.6341
191 6DEN TP9 14.8084
192 6DEN G8A 14.8084
193 6DEN FAD 14.8084
194 2NXW TPP 16.6372
195 6FC1 MGP 17.1875
196 4V1F BQ1 18.6047
197 5YV5 ADP 33.3333
Pocket No.: 2; Query (leader) PDB : 5ESO; Ligand: TDP; Similar sites found with APoc: 197
This union binding pocket(no: 2) in the query (biounit: 5eso.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
1 4A59 AMP 1.21951
2 1ZPD DPX 1.23239
3 3AJM 4IP 1.87793
4 2C42 TPP 1.91638
5 2C42 PYR 1.91638
6 4KVL PLM 1.91638
7 4YJ1 ADP 1.91638
8 1TKB N1T 2.09059
9 5EGH PC 2.0979
10 1NLM UD1 2.1978
11 1TE2 PGA 2.21239
12 1R9J TPP 2.26481
13 1KRH FAD 2.36686
14 1J78 OLA 2.40175
15 5B48 TDN 2.43902
16 1R2J FAD 2.45902
17 2DE4 BPS 2.46575
18 5N6N SUC 2.5
19 9ABP GLA 2.61438
20 9ABP GAL 2.61438
21 4YDS ATP 2.63158
22 4CCW VKC 2.67559
23 3I7S PYR 2.73973
24 4D5G FAD 2.78746
25 4D5G TPP 2.78746
26 5ND5 TPP 2.78746
27 3AI7 TPP 2.78746
28 5TBS ADE 2.78746
29 3OBK PBG 2.80899
30 1PFK ADP 2.8125
31 1GDE GLU PLP 2.82776
32 5W3Y ACO 2.84091
33 5CGE 51F 2.88809
34 4NTO 1PW 2.89855
35 1RJW ETF 2.94985
36 3IHB GLU 2.96167
37 1KAR HSM 2.99539
38 3U7Q HCA 3.04878
39 3BRE C2E 3.07263
40 3W9F I3P 3.07692
41 2OG7 AHB 3.08123
42 2O1S TDP 3.13589
43 1ITZ TPP 3.13589
44 2IYA UDP 3.13589
45 1D8C GLV 3.13589
46 4G05 JZ3 3.15457
47 4G86 BNT 3.16901
48 5G1N PAL 3.18471
49 3LL5 IP8 3.21285
50 3IT7 TLA 3.2967
51 3B8I OXL 3.3101
52 2VK4 TPP 3.37478
53 5NM7 GLY 3.38346
54 4PPF FLC 3.42857
55 4WZ6 ATP 3.44828
56 3WW2 SF9 3.51562
57 3MMH SME 3.59281
58 4WJT NAG 3.59281
59 1U3G ADP 3.7037
60 3B5J 12D 3.7037
61 1QPB PYM 3.73002
62 1QPB TPP 3.73002
63 4NV0 MG7 3.76176
64 4JZ8 CIT 3.78549
65 5B47 PYR 3.83275
66 5B47 TPP 3.83275
67 2YIC TPP 3.83275
68 5OKU 0L1 3.89222
69 3A51 VDY 3.89294
70 2Q8M AMP 3.91566
71 2BOY BHO 3.93701
72 3FJG 3PG 3.98406
73 2CE7 ADP 4.00697
74 2NSX IFM 4.00697
75 1RP7 TZD 4.00697
76 1UMD TDP COI 4.01235
77 2OZL TPP 4.10557
78 3S2U UD1 4.10959
79 5C9P FUC 4.19948
80 1BW9 PPY 4.21348
81 1OHE ACE ALA SEP PRO 4.31034
82 4AVV GHE 4.41176
83 4AVV CD 4.41176
84 4HE2 AMP 4.43787
85 3KC1 2T6 4.45104
86 2B99 RDL 4.48718
87 2O1C PPV 4.66667
88 1V5F TPP 4.70383
89 1V5F FAD 4.70383
90 1EJH M7G 4.73684
91 2QV7 ADP 4.74777
92 6CEP OXM 4.79042
93 5A96 GTP 4.81928
94 4OFG PCG 4.86111
95 6MFL OPV 4.87013
96 2J5V PCA 4.90463
97 2Q8G AZX 4.914
98 3KO0 TFP 4.9505
99 1T36 ORN 4.97382
100 4K79 GAL A2G 5
101 1W6F ISZ 5.03597
102 2FV1 GAD NDG 5.03979
103 2P3V SRT 5.07812
104 2C3H GLC GLC 5.10204
105 5AGR A52 5.17241
106 3NFD COA 5.22876
107 2JAP J01 5.26316
108 3EGI ADP 5.33981
109 4JCA CIT 5.38922
110 4R5Z PMP 5.44959
111 2UZH CDP 5.45455
112 1NXJ TLA 5.46448
113 1RRV TYD 5.52885
114 5KL0 G16 5.56745
115 3LTW HLZ 5.57491
116 5C8W PCG 5.59441
117 1G2O IMH 5.59701
118 3SHR CMP 5.68562
119 3DVA TPW 5.69106
120 1XVB 3BR 5.6926
121 3H4T UDP 5.69307
122 1W85 TDP 5.70652
123 4KGD TDP 5.74913
124 4KGD FAD 5.74913
125 2R0D 4IP 5.76369
126 2R09 4IP 5.76369
127 2J0W ASP 5.79065
128 3EYA TDP 6.01093
129 1LES GLC FRU 6.07735
130 6CZY PMP 6.07735
131 5URY PAM 6.16438
132 2Q28 TPP 6.20567
133 2ACV UDP 6.2635
134 5VEQ PMP 6.56934
135 6FBA D48 6.59026
136 2C31 TZD 6.69014
137 2C31 ADP 6.69014
138 4R78 AMP 6.79612
139 3ITJ CIT 6.80473
140 3EXH TPP 6.80628
141 4WBD CIT 6.83919
142 2A5F NAD 7.42857
143 3FSJ D7K 7.57576
144 4UEC MGT 7.69231
145 2BO4 FLC 7.80856
146 5T48 MGP 7.8125
147 2VBF TPP 8.24561
148 3NOJ PYR 8.40336
149 3IAE D7K 8.53659
150 6G47 SIA SIA 8.61244
151 2OG2 MLI 8.6351
152 2UZ1 TPP 8.70337
153 2IHT TPP 8.726
154 1UPA TPP 8.726
155 2W97 MGO 8.75576
156 4HSE ADP 8.81612
157 1H5R THM 8.87372
158 2IHU TP9 8.90052
159 3X27 TRP 8.95522
160 4YEF 4CQ 8.98876
161 1H5S TMP 9.21502
162 1Z0N BCD 9.375
163 5EXE 5SR 9.52381
164 5AHW CMP 9.52381
165 1YBH P22 9.58188
166 2PZE ATP 9.60699
167 2O66 FLC 9.62963
168 4QS9 BGC 9.70464
169 4UDK BMA 9.79827
170 1YQT ADP 9.8513
171 1OZH HE3 9.93031
172 5T46 MGP 10.6061
173 1WAP TRP 10.6667
174 1JJ7 ADP 10.7692
175 4RJK TPP 11.3835
176 4RJK TDL 11.3835
177 2AWN ADP 12.0735
178 4JNJ BTN 12.1739
179 5E5U MLI 12.5628
180 5FII PHE 12.7451
181 1LVW TYD 12.8814
182 1T0S BML 13.9535
183 5WKC TP9 14.1115
184 5WKC AUJ 14.1115
185 1T9D P25 14.1115
186 1T9D FAD 14.1115
187 1T9D 1MM 14.1115
188 1T9D P22 14.1115
189 1T9D PYD 14.1115
190 5ABX MGP 14.6341
191 6DEN TP9 14.8084
192 6DEN G8A 14.8084
193 6DEN FAD 14.8084
194 2NXW TPP 16.6372
195 6FC1 MGP 17.1875
196 4V1F BQ1 18.6047
197 5YV5 ADP 33.3333
Pocket No.: 3; Query (leader) PDB : 5ESO; Ligand: TDP; Similar sites found with APoc: 30
This union binding pocket(no: 3) in the query (biounit: 5eso.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
1 1LFO OLA None
2 1RRC ADP 1.66113
3 6BK3 UDP 1.92719
4 1B4N GUA 2.26481
5 1RV1 IMZ 2.35294
6 2AJH MET 2.55102
7 5DNC ASN 2.61324
8 1ZGS XMM 2.68456
9 1PCA CIT 2.72953
10 2R5N RP5 2.78746
11 2R5N R5P 2.78746
12 2R5N TPP 2.78746
13 3JU6 ARG 2.97297
14 4K47 WMP 3.64583
15 1G8S MET 3.65854
16 3EF0 ALF 4.30108
17 1GVF PGH 4.54545
18 2F7A BEZ 4.74138
19 1GPM CIT 5.57491
20 3BRN SRO 5.73248
21 1V1A KDG 5.82524
22 1P0Z FLC 6.10687
23 3HY2 ATP 6.36364
24 4KQP GLN 6.46552
25 5AJU RP5 8.0292
26 3C0G 3AM 8.83191
27 5WQJ 7N3 12.1212
28 5HZX 2GE 14.2045
29 6BR7 BEF 14.2857
30 5XNA SHV 21.7391
Pocket No.: 4; Query (leader) PDB : 5ESO; Ligand: ISC; Similar sites found with APoc: 30
This union binding pocket(no: 4) in the query (biounit: 5eso.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
1 1LFO OLA None
2 1RRC ADP 1.66113
3 6BK3 UDP 1.92719
4 1B4N GUA 2.26481
5 1RV1 IMZ 2.35294
6 2AJH MET 2.55102
7 5DNC ASN 2.61324
8 1ZGS XMM 2.68456
9 1PCA CIT 2.72953
10 2R5N RP5 2.78746
11 2R5N R5P 2.78746
12 2R5N TPP 2.78746
13 3JU6 ARG 2.97297
14 4K47 WMP 3.64583
15 1G8S MET 3.65854
16 3EF0 ALF 4.30108
17 1GVF PGH 4.54545
18 2F7A BEZ 4.74138
19 1GPM CIT 5.57491
20 3BRN SRO 5.73248
21 1V1A KDG 5.82524
22 1P0Z FLC 6.10687
23 3HY2 ATP 6.36364
24 4KQP GLN 6.46552
25 5AJU RP5 8.0292
26 3C0G 3AM 8.83191
27 5WQJ 7N3 12.1212
28 5HZX 2GE 14.2045
29 6BR7 BEF 14.2857
30 5XNA SHV 21.7391
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