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Receptor
PDB id Resolution Class Description Source Keywords
4K49 1.89 Å EC: 3.1.-.- X-RAY CRYSTAL STRUCTURE OF E. COLI YDII COMPLEXED WITH 2,4- DIHYDROXYPHENACYL COA ESCHERICHIA COLI HOT-DOG FOLD THIOESTERASE HYDROLASE
Ref.: STRUCTURE AND CATALYSIS IN THE ESCHERICHIA COLI HOT THIOESTERASE PARALOGS YDII AND YBDB. BIOCHEMISTRY V. 53 4788 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
HFQ B:201;
C:201;
A:201;
D:201;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 Ki = 2.5 uM
917.666 C29 H42 N7 O19 P3 S CC(C)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4K49 1.89 Å EC: 3.1.-.- X-RAY CRYSTAL STRUCTURE OF E. COLI YDII COMPLEXED WITH 2,4- DIHYDROXYPHENACYL COA ESCHERICHIA COLI HOT-DOG FOLD THIOESTERASE HYDROLASE
Ref.: STRUCTURE AND CATALYSIS IN THE ESCHERICHIA COLI HOT THIOESTERASE PARALOGS YDII AND YBDB. BIOCHEMISTRY V. 53 4788 2014
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 19 families.
1 4K4B Ki = 12.2 uM UOQ C32 H56 N7 O17 P3 S CCCCCCCCCC....
2 4K49 Ki = 2.5 uM HFQ C29 H42 N7 O19 P3 S CC(C)(CO[P....
3 4K4A Ki = 7.8 uM 0FQ C29 H42 N7 O17 P3 S CC(C)(CO[P....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 4K4C Ki = 65 uM 0FQ C29 H42 N7 O17 P3 S CC(C)(CO[P....
2 4K4D Ki = 5.9 uM HFQ C29 H42 N7 O19 P3 S CC(C)(CO[P....
3 4K4B Ki = 12.2 uM UOQ C32 H56 N7 O17 P3 S CCCCCCCCCC....
4 4K49 Ki = 2.5 uM HFQ C29 H42 N7 O19 P3 S CC(C)(CO[P....
5 4K4A Ki = 7.8 uM 0FQ C29 H42 N7 O17 P3 S CC(C)(CO[P....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 4K4C Ki = 65 uM 0FQ C29 H42 N7 O17 P3 S CC(C)(CO[P....
2 4K4D Ki = 5.9 uM HFQ C29 H42 N7 O19 P3 S CC(C)(CO[P....
3 4K4B Ki = 12.2 uM UOQ C32 H56 N7 O17 P3 S CCCCCCCCCC....
4 4K49 Ki = 2.5 uM HFQ C29 H42 N7 O19 P3 S CC(C)(CO[P....
5 4K4A Ki = 7.8 uM 0FQ C29 H42 N7 O17 P3 S CC(C)(CO[P....
6 4M20 - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: HFQ; Similar ligands found: 121
No: Ligand ECFP6 Tc MDL keys Tc
1 HFQ 1 1
2 SOP 0.843284 0.955556
3 4CO 0.829787 0.988764
4 CMC 0.823529 0.955556
5 01A 0.811189 0.935484
6 0FQ 0.804196 0.977528
7 COF 0.794326 0.934783
8 COS 0.792593 0.934066
9 CAO 0.792593 0.923913
10 ACO 0.781022 0.923913
11 4CA 0.776224 0.988764
12 UOQ 0.77551 0.934783
13 NHM 0.77551 0.934783
14 NHW 0.77551 0.934783
15 A1S 0.77305 0.955556
16 2CP 0.762238 0.945055
17 CO6 0.758865 0.934066
18 0T1 0.757353 0.933333
19 3KK 0.757143 0.934066
20 FYN 0.757143 0.955056
21 3CP 0.756944 0.955556
22 OXK 0.751773 0.934066
23 COK 0.751773 0.934066
24 BCA 0.751724 0.966667
25 MC4 0.75 0.885417
26 2NE 0.748299 0.977778
27 CIC 0.748299 0.955556
28 BCO 0.748252 0.934066
29 1VU 0.746479 0.923913
30 COA 0.744526 0.955056
31 DCA 0.742647 0.912088
32 2MC 0.741259 0.894737
33 30N 0.741007 0.876289
34 0ET 0.738255 0.934783
35 3HC 0.736111 0.944444
36 MLC 0.736111 0.934066
37 1HE 0.736111 0.934783
38 IVC 0.736111 0.944444
39 CS8 0.733333 0.924731
40 COW 0.732877 0.966667
41 IRC 0.732877 0.944444
42 CAA 0.731034 0.944444
43 MCA 0.731034 0.923913
44 COO 0.731034 0.934066
45 ETB 0.729927 0.880435
46 TGC 0.72973 0.945055
47 AMX 0.728571 0.94382
48 NHQ 0.727273 0.966292
49 SCA 0.726027 0.934066
50 SCO 0.723404 0.933333
51 CMX 0.723404 0.933333
52 HXC 0.722973 0.913979
53 1GZ 0.721088 0.923913
54 HGG 0.721088 0.934066
55 2KQ 0.721088 0.913979
56 BYC 0.721088 0.955556
57 FAM 0.71831 0.913043
58 FCX 0.71831 0.903226
59 FAQ 0.716216 0.955556
60 MCD 0.715278 0.913043
61 01K 0.713376 0.955556
62 CO8 0.713333 0.913979
63 HAX 0.713287 0.913043
64 GRA 0.711409 0.934066
65 WCA 0.710526 0.956044
66 COT 0.708861 0.977528
67 UCC 0.708609 0.913979
68 5F9 0.708609 0.913979
69 ST9 0.708609 0.913979
70 MFK 0.708609 0.913979
71 MYA 0.708609 0.913979
72 DCC 0.708609 0.913979
73 YE1 0.707483 0.966292
74 HDC 0.705882 0.913979
75 SCD 0.705479 0.933333
76 CA6 0.703448 0.868687
77 1CZ 0.701987 0.923913
78 S0N 0.701987 0.955556
79 NMX 0.69863 0.865979
80 4KX 0.694805 0.924731
81 CAJ 0.693878 0.913043
82 MRR 0.690323 0.913979
83 MRS 0.690323 0.913979
84 1CV 0.688312 0.934066
85 1HA 0.685535 0.977778
86 8Z2 0.681529 0.904255
87 CA5 0.678788 0.935484
88 CA8 0.675497 0.868687
89 YNC 0.675159 0.923913
90 DAK 0.675159 0.945652
91 CA3 0.668712 0.977528
92 F8G 0.666667 0.895833
93 93M 0.654971 0.966667
94 7L1 0.653061 0.923913
95 93P 0.64497 0.966667
96 CCQ 0.636943 0.914894
97 CO7 0.619355 0.934066
98 UCA 0.616279 0.934783
99 COD 0.606897 0.94382
100 5TW 0.592391 0.895833
101 4BN 0.592391 0.895833
102 OXT 0.581522 0.915789
103 ASP ASP ASP ILE CMC NH2 0.553672 0.913043
104 JBT 0.552083 0.896907
105 BSJ 0.545455 0.945652
106 PLM COA 0.541667 0.882979
107 COA PLM 0.541667 0.882979
108 HMG 0.538922 0.902174
109 ACE SER ASP ALY THR NH2 COA 0.502591 0.913043
110 PAP 0.5 0.775281
111 PPS 0.467626 0.721649
112 SFC 0.461111 0.934783
113 RFC 0.461111 0.934783
114 191 0.459302 0.85
115 A3P 0.455224 0.764045
116 0WD 0.447205 0.774194
117 PUA 0.408284 0.804348
118 PTJ 0.407895 0.833333
119 A22 0.405405 0.797753
120 PAJ 0.4 0.844444
121 3AM 0.4 0.752809
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4K49; Ligand: HFQ; Similar sites found with APoc: 155
This union binding pocket(no: 1) in the query (biounit: 4k49.bio1) has 67 residues
No: Leader PDB Ligand Sequence Similarity
1 2CYE COA None
2 4YEF 4CQ None
3 1LR8 IHS None
4 1PN4 HDC None
5 1PTR PRB None
6 1Z0N BCD None
7 3I7V B4P None
8 1TUK PGM None
9 4IEN COA None
10 3IP8 B85 None
11 3KPE TM3 None
12 4EKQ NPO None
13 1VC9 ATP None
14 1L7N ALF None
15 1L7N AF3 None
16 3DAK ANP None
17 4K55 H6P None
18 1JOC ITP None
19 4YEE 4CQ None
20 3NFD COA None
21 3LQV ADE None
22 3EW2 BTN None
23 5JBX MLI 1.47059
24 5G3R 89A 1.47059
25 1A5Z FBP 1.5674
26 5FDZ 5X0 1.68067
27 5ML0 P2L 1.81818
28 4MZQ 1VU 2.20588
29 1IZC PYR 2.20588
30 5LVP ATP 2.20588
31 3GD8 GOL 2.20588
32 3JRS A8S 2.20588
33 1GYY FHC 2.63158
34 2G30 ALA ALA PHE 2.94118
35 1O9U ADZ 2.94118
36 4IA6 EIC 2.94118
37 1NE7 16G 2.94118
38 2WEL K88 2.94118
39 2V7O DRN 2.94118
40 1KQR MNA 2.94118
41 2VSS V55 2.94118
42 2VN9 GVD 2.94118
43 1EHH NAG NAG NAG 3.37079
44 5U6V 7WY 3.63636
45 2Z49 AMG 3.67647
46 2Z48 A2G 3.67647
47 6EK3 OUL 3.67647
48 5NCB JZ3 3.67647
49 5NC1 NAG 3.67647
50 2Z48 NGA 3.67647
51 4CT7 TRP 3.67647
52 3TD3 GLY 4.06504
53 4KBA 1QM 4.41176
54 1LVW TYD 4.41176
55 5E5U 1PS 4.41176
56 2W9S TOP 4.41176
57 1ELI PYC 4.41176
58 1C3V PDC 4.41176
59 6G47 SIA 4.41176
60 3GFS FMN 4.41176
61 3EZ2 ADP 4.41176
62 4HZO COA 5.14706
63 3KV8 FAH 5.14706
64 6GSG RCO 5.14706
65 4OUJ LBT 5.14706
66 2GJ5 VD3 5.14706
67 5WSY 7UC 5.14706
68 2OI2 DP6 5.14706
69 1C1X HFA 5.14706
70 4RF7 ARG 5.14706
71 1KC7 PPR 5.14706
72 2ZV2 609 5.14706
73 5C9P FUC 5.14706
74 4XH0 ADP 5.14706
75 1I0B PEL 5.14706
76 5NJI 8Z2 5.88235
77 1MJT ITU 5.88235
78 1H5R THM 5.88235
79 1H5S TMP 5.88235
80 4LO2 GAL BGC 5.88235
81 4CL6 7SB 5.88235
82 1J84 BGC BGC BGC BGC 5.88235
83 5YW5 ADE 5.88235
84 3KDM TES 5.88235
85 2R0D 4IP 5.88235
86 1IZO PAM 5.88235
87 2R09 4IP 5.88235
88 1WDA BAG 5.88235
89 4KAX 4IP 5.88235
90 1MJT NAD 5.88235
91 3GDN MXN 5.88235
92 2PTM CMP 5.88235
93 5HVJ ANP 5.88235
94 6D6Y SAH 5.88235
95 1FHX 4IP 6.20155
96 4CS9 AMP 6.61765
97 4U8P UDP 6.61765
98 4M6T SAM 6.61765
99 5FQK 6NT 6.61765
100 2YYE APC 6.61765
101 1U25 IHS 6.61765
102 2QLU ADE 6.61765
103 3AKI AH8 7.35294
104 1H3F TYE 7.35294
105 5FBK TCR 7.35294
106 1ZDQ MSM 7.7381
107 5FH7 5XL 8.06452
108 5FCF GLY GLY GLY 8.08823
109 3H11 ALA ILE GLU THR ASA 8.08823
110 5T8U LPA 8.08823
111 1FAO 4IP 8.73016
112 1ZGS XMM 8.82353
113 4LIK CIT 8.82353
114 5DMM HCS 8.82353
115 1ON3 DXX 8.82353
116 4DO1 ANN 8.82353
117 1WAP TRP 9.33333
118 3E7S AT2 9.55882
119 2EB5 OXL 9.55882
120 2WDQ TEO 9.56522
121 4R4U COA 10.2941
122 2BHW NEX 10.2941
123 2CXG GLC GLC 10.2941
124 1F6D UDP 10.2941
125 5UPK ANP 10.2941
126 4CQK PIO 10.6383
127 1ULM NAG NAG NAG 10.9756
128 4DC2 ADE 11.0294
129 4N2R AHR 11.7647
130 3AB4 THR 11.7647
131 1XPJ TLA 11.9048
132 4O08 PO6 12.5
133 3NJQ NJQ 12.5
134 6E1Q CFA 12.5
135 2NVK NAP 12.5
136 2V1O COA 12.5
137 1RV1 IMZ 12.9412
138 3HQP OXL 13.2353
139 4GAH 0ET 13.9706
140 4L80 OXL 13.9706
141 5OF1 SAL 14.7059
142 1VPM COA 15.4412
143 5OSW DIU 15.4412
144 4UP5 94W 17.1717
145 3UKR CKH 17.6471
146 2I74 MAN MAN MAN MAN 17.6471
147 1WN3 HXC 18.3824
148 3KLL MAL 18.3824
149 1JT2 FER 19.1176
150 3F5O UOC COA 22.0588
151 2H88 TEO 25
152 4C2W ANP 28.8462
153 5HMC 5NE 37.5
154 4ZRB COA 38.2353
155 3R35 4CO 41.9118
Pocket No.: 2; Query (leader) PDB : 4K49; Ligand: HFQ; Similar sites found with APoc: 32
This union binding pocket(no: 2) in the query (biounit: 4k49.bio1) has 57 residues
No: Leader PDB Ligand Sequence Similarity
1 4WGF HX2 None
2 3PTG 932 1.47059
3 3LKF PC 1.47059
4 5MLJ 9ST 1.78571
5 5X80 SAL 2.94118
6 5L4R CPT 3.67647
7 1SC3 MLI 3.67647
8 3WWX DIA 4.41176
9 4XFM THE 4.41176
10 3CTY FAD 4.41176
11 2F2U M77 4.41176
12 4ISS TAR 5.14706
13 4M1U A2G MBG 5.14706
14 1BW9 PPY 5.14706
15 4XMF HSM 5.88235
16 3AQT RCO 5.88235
17 2GKS ADP 5.88235
18 1ZPD CIT 5.88235
19 3B9Z CO2 6.61765
20 3CF6 SP1 7.35294
21 5V3Y 5V8 8.08823
22 5L8L ADP 9.40171
23 5WXU FLC 9.55882
24 1KNM LAT 10.7692
25 5VE5 GSH 11.7647
26 5LX9 OLB 12.5
27 3BJK CIT 12.5
28 6H8S FSZ 12.5
29 2F2H XTG 13.9706
30 1VBO MAN MAN MAN 14.7059
31 6MJ7 ARG 16.3636
32 5KBZ 3B2 16.9118
Pocket No.: 3; Query (leader) PDB : 4K49; Ligand: HFQ; Similar sites found with APoc: 52
This union binding pocket(no: 3) in the query (biounit: 4k49.bio2) has 64 residues
No: Leader PDB Ligand Sequence Similarity
1 3AJ4 SEP None
2 2BS5 BGC GAL FUC None
3 4GN8 ASO 2.20588
4 3W9K MYR 2.20588
5 5YRM BGC GLC 2.20588
6 4B4Q A2G GAL NAG FUC GAL GLC 2.94118
7 1JPA ANP 3.67647
8 5OM2 DXT 3.67647
9 1T5C ADP 3.67647
10 5E5U MLI 4.41176
11 4ARE FLC 4.41176
12 1G41 ADP 4.41176
13 4WOE 3S5 4.41176
14 4Y4V DAL 4.41176
15 4XUB 43D 5.12821
16 4LJ9 ACP 5.14706
17 5YLF BGC 5.14706
18 4WCX MET 5.14706
19 2ZWI C5P 5.14706
20 6CGN DA 5.14706
21 4FCW ADP 5.14706
22 1QXA GLY GLY GLY 5.14706
23 5D2H AKG 5.14706
24 5MUL BDP 5.88235
25 2QPU QPU 5.88235
26 5TSH ANP 5.88235
27 3VU2 CEX 5.88235
28 5TSH ADP 5.88235
29 1GXS BEZ 5.88235
30 3SZB I1E 5.88235
31 1EB9 HBA 5.88235
32 4MCC 21X 5.88235
33 3GYQ SAM 5.88235
34 5NM7 GLY 5.88235
35 1TL2 NDG 6.61765
36 6GNO XDI 6.66667
37 3LN9 FLC 7.35294
38 4IHQ ADP 7.35294
39 1R6B ADP 7.35294
40 2QIE 8CS 7.79221
41 6APL C5P 8.08823
42 2QEH SRO 8.82353
43 5Z5I XYP 9.55882
44 4USI AKG 9.55882
45 5AOG IAC 9.55882
46 3ZXE PGZ 10.5263
47 1TMX BEZ 11.0294
48 1GXU 2HP 13.1868
49 5GQI ATP 13.9706
50 2CDO GAL AAL GAL AAL GAL AAL 13.9706
51 4NTO 1PW 17.6471
52 1UYY BGC BGC 19.084
Pocket No.: 4; Query (leader) PDB : 4K49; Ligand: HFQ; Similar sites found with APoc: 36
This union binding pocket(no: 4) in the query (biounit: 4k49.bio2) has 56 residues
No: Leader PDB Ligand Sequence Similarity
1 6EOM ALA LYS None
2 4GLW NMN None
3 1QKQ MAN None
4 1N13 AG2 None
5 3ZO7 K6H None
6 4FHT DHB None
7 4AGS GSH 1.47059
8 2XYA 7L4 1.47059
9 3LGS SAH 2.20588
10 5OCG 9R5 2.20588
11 5H2U 1N1 2.20588
12 2HK9 SKM 2.94118
13 3QH2 3NM 4.41176
14 5AHW CMP 4.41176
15 6FYQ PLP 4.95868
16 3X01 AMP 5.14706
17 2H5Z CTO 6.55738
18 3WCS MAN NAG GAL 6.61765
19 5MB4 NDG 6.61765
20 2XDQ MGX 7.35294
21 5VZ0 2BA 7.35294
22 3E3U NVC 7.35294
23 1Q8P MAN MMA 8.08823
24 2PHR MAN MAN 8.08823
25 1GQ2 OXL 8.82353
26 1G6O ADP 8.82353
27 3O5N BR0 9.82143
28 4UP4 NDG 11.0294
29 6MDE MEV 11.0294
30 4J0Q GDP 12.5
31 5T52 NGA 13.2353
32 1Q19 SSC 13.9706
33 5WZE PRO 14.7059
34 6HKE LMR 15.4412
35 2ZQO NGA 17.6923
36 5FII PHE 23.5294
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