Receptor
PDB id Resolution Class Description Source Keywords
4K4D 2.17 Å EC: 3.1.2.- X-RAY CRYSTAL STRUCTURE OF E. COLI YBDB COMPLEXED WITH 2,4- DIHYDROXYPHENACYL-COA ESCHERICHIA COLI HOTDOG FOLD THIOEATSRASE 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
ACT B:202;
B:203;
Invalid;
Invalid;
none;
none;
submit data
59.044 C2 H3 O2 CC(=O...
HFQ B:201;
A:201;
Valid;
Valid;
none;
none;
Ki = 5.9 uM
917.666 C29 H42 N7 O19 P3 S CC(C)...
MLI A:202;
Valid;
none;
submit data
102.046 C3 H2 O4 C(C(=...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4K4D 2.17 Å EC: 3.1.2.- X-RAY CRYSTAL STRUCTURE OF E. COLI YBDB COMPLEXED WITH 2,4- DIHYDROXYPHENACYL-COA ESCHERICHIA COLI HOTDOG FOLD THIOEATSRASE HYDROLASE
Ref.: STRUCTURE AND CATALYSIS IN THE ESCHERICHIA COLI HOT THIOESTERASE PARALOGS YDII AND YBDB. BIOCHEMISTRY V. 53 4788 2014
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 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....
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: 119
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 CAO 0.792593 0.923913
9 COS 0.792593 0.934066
10 ACO 0.781022 0.923913
11 4CA 0.776224 0.988764
12 UOQ 0.77551 0.934783
13 NHW 0.77551 0.934783
14 NHM 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 COK 0.751773 0.934066
23 OXK 0.751773 0.934066
24 BCA 0.751724 0.966667
25 MC4 0.75 0.885417
26 CIC 0.748299 0.955556
27 2NE 0.748299 0.977778
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 IRC 0.732877 0.944444
41 COW 0.732877 0.966667
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 BYC 0.721088 0.955556
54 1GZ 0.721088 0.923913
55 2KQ 0.721088 0.913979
56 HGG 0.721088 0.934066
57 FCX 0.71831 0.903226
58 FAM 0.71831 0.913043
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 ST9 0.708609 0.913979
68 MFK 0.708609 0.913979
69 5F9 0.708609 0.913979
70 UCC 0.708609 0.913979
71 DCC 0.708609 0.913979
72 MYA 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 MRS 0.690323 0.913979
83 MRR 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 DAK 0.675159 0.945652
90 YNC 0.675159 0.923913
91 CA3 0.668712 0.977528
92 93M 0.654971 0.966667
93 93P 0.64497 0.966667
94 CCQ 0.636943 0.914894
95 CO7 0.619355 0.934066
96 UCA 0.616279 0.934783
97 COD 0.606897 0.94382
98 4BN 0.592391 0.895833
99 5TW 0.592391 0.895833
100 OXT 0.581522 0.915789
101 JBT 0.552083 0.896907
102 BSJ 0.545455 0.945652
103 COA PLM 0.541667 0.882979
104 COA MYR 0.541667 0.882979
105 PLM COA 0.541667 0.882979
106 HMG 0.538922 0.902174
107 PAP 0.5 0.775281
108 ACE SER ASP ALY THR NH2 COA 0.497462 0.913043
109 PPS 0.467626 0.721649
110 RFC 0.461111 0.934783
111 SFC 0.461111 0.934783
112 191 0.459302 0.85
113 A3P 0.455224 0.764045
114 0WD 0.447205 0.774194
115 PUA 0.408284 0.804348
116 PTJ 0.407895 0.833333
117 A22 0.405405 0.797753
118 3AM 0.4 0.752809
119 PAJ 0.4 0.844444
Ligand no: 2; Ligand: MLI; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 MLI 1 1
2 OAA 0.5 0.666667
3 SIN 0.5 0.785714
4 OXL 0.416667 0.642857
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4K4D; Ligand: HFQ; Similar sites found: 37
This union binding pocket(no: 1) in the query (biounit: 4k4d.bio1) has 45 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1PTR PRB 0.008391 0.43322 None
2 3NW7 LGV 0.00991 0.41951 None
3 3BP1 GUN 0.01262 0.41688 None
4 3DAK ANP 0.008184 0.40246 None
5 2WQ4 SFU 0.01939 0.40123 None
6 4AVB CMP 0.01348 0.40343 1.45985
7 4MZQ 1VU 0.00001096 0.51047 2.91971
8 5HVJ ANP 0.01049 0.42374 2.91971
9 1O9U ADZ 0.0008377 0.48834 3.64964
10 5NJI 8Z2 0.0000004543 0.59135 4.37956
11 4HZO COA 0.0001973 0.41048 4.37956
12 2Z49 AMG 0.006622 0.43448 5.10949
13 4LO2 GAL BGC 0.01823 0.41885 5.10949
14 2Z48 NGA 0.02353 0.41188 5.10949
15 1A5Z FBP 0.00996 0.42392 5.83942
16 4CS9 AMP 0.01978 0.41752 5.83942
17 4XH0 ADP 0.01417 0.4179 6.56934
18 1LR8 IHS 0.007502 0.44079 6.75676
19 1PN4 HDC 0.00001338 0.46443 7.29927
20 2QLU ADE 0.00541 0.43848 7.29927
21 4IZC 1GZ 0.0059 0.41831 7.29927
22 4GAH 0ET 0.000007418 0.48304 8.0292
23 3B9Z CO2 0.004167 0.44868 8.75912
24 4CL6 7SB 0.000941 0.43764 8.75912
25 4YMJ 4EJ 0.01921 0.40974 8.75912
26 5KBZ 3B2 0.0002429 0.48303 10.219
27 3CV2 COA 0.03247 0.40584 10.9489
28 1N62 MCN 0.01584 0.40344 11.6788
29 3LQV ADE 0.01541 0.40629 15.3846
30 4R4U COA 0.0009463 0.43553 17.5182
31 4PYW ACE THR THR ALA ILE NH2 0.006797 0.40441 20.438
32 1N13 AG2 0.02001 0.4093 24.7788
33 1WN3 HXC 0.000000395 0.53391 25
34 2QQC AG2 0.02316 0.40589 25
35 3F5O UOC COA 0.0000001575 0.61144 27.0073
36 4ZRB COA 0.000003157 0.5224 27.0073
37 3R35 4CO 0.0003748 0.50318 40.8759
Pocket No.: 2; Query (leader) PDB : 4K4D; Ligand: MLI; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4k4d.bio1) has 2 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4K4D; Ligand: HFQ; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4k4d.bio1) has 45 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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