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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: 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
Ligand no: 2; Ligand: MLI; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 MLI 1 1
2 OAA 0.5 0.666667
3 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 with APoc: 86
This union binding pocket(no: 1) in the query (biounit: 4k4d.bio1) has 45 residues
No: Leader PDB Ligand Sequence Similarity
1 1Z0N BCD None
2 1PTR PRB None
3 1K3A ACP None
4 4RJD TFP None
5 3NW7 LGV None
6 3BP1 GUN None
7 3DAK ANP None
8 2RI1 GLP None
9 5DBX ANP None
10 2XVD AS6 None
11 2WQ4 SFU None
12 1TUK PGM None
13 4AVB CMP 1.45985
14 3D04 SAK 2.18978
15 4MZQ 1VU 2.91971
16 4WGF HX2 2.91971
17 5HVJ ANP 2.91971
18 5UPK ANP 2.91971
19 2IRY DGT 2.91971
20 3VHE 42Q 2.91971
21 5X80 SAL 2.91971
22 1O9U ADZ 3.64964
23 3E7S AT2 3.64964
24 3N8K D1X 3.64964
25 4EZW ASN ARG LEU LEU LEU THR GLY 3.64964
26 3BZ3 YAM 3.64964
27 5NJI 8Z2 4.37956
28 4HZO COA 4.37956
29 1H5R THM 4.37956
30 1H5S TMP 4.37956
31 4IEN COA 4.37956
32 1ZPD CIT 4.37956
33 2X2M X2M 4.37956
34 6AC9 ANP 4.37956
35 2Z49 AMG 5.10949
36 2Z48 A2G 5.10949
37 4LO2 GAL BGC 5.10949
38 2Z48 NGA 5.10949
39 3G4Q MCH 5.10949
40 4CS9 AMP 5.83942
41 1A5Z FBP 5.83942
42 3AB4 THR 5.83942
43 4NFE BEN 5.83942
44 4OUJ LBT 5.83942
45 6CGN DA 6.56934
46 4XH0 ADP 6.56934
47 5XLS URA 6.56934
48 1JPA ANP 6.56934
49 1LR8 IHS 6.75676
50 3KV8 FAH 7.29927
51 1PN4 HDC 7.29927
52 2QLU ADE 7.29927
53 1LVW TYD 7.29927
54 4IZC 1GZ 7.29927
55 4GAH 0ET 8.0292
56 2V1O COA 8.0292
57 3B9Z CO2 8.75912
58 4CL6 7SB 8.75912
59 3NJQ NJQ 8.75912
60 4YMJ 4EJ 8.75912
61 3W6X HZP 8.75912
62 4YEE 4CQ 8.88889
63 6GSG RCO 9.48905
64 3UKR CKH 9.48905
65 5L8L ADP 9.48905
66 5KBZ 3B2 10.219
67 2GKS ADP 10.219
68 4DC2 ADE 10.7143
69 3CV2 COA 10.9489
70 1N62 MCN 11.6788
71 3DLS ADP 11.6788
72 4YEF 4CQ 12.3596
73 5GQX GLC GLC GLC GLC 12.4088
74 2WEL K88 13.1387
75 4C2W ANP 13.1387
76 3LQV ADE 15.3846
77 4R4U COA 17.5182
78 4PYW ACE THR THR ALA ILE NH2 20.438
79 3CF6 SP1 21.1679
80 2HIM ASN 24.0876
81 1N13 AG2 24.7788
82 1WN3 HXC 25
83 2QQC AG2 25
84 3F5O UOC COA 27.0073
85 4ZRB COA 27.0073
86 3R35 4CO 40.8759
Pocket No.: 2; Query (leader) PDB : 4K4D; Ligand: MLI; Similar sites found with APoc: 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 Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4K4D; Ligand: HFQ; Similar sites found with APoc: 57
This union binding pocket(no: 3) in the query (biounit: 4k4d.bio1) has 45 residues
No: Leader PDB Ligand Sequence Similarity
1 1TL2 NDG None
2 2WJG GDP None
3 1EN2 NAG NAG NAG NAG None
4 3DUV KDO None
5 6EK3 OUL 0.904977
6 1T3D CYS 2.18978
7 1L7N AF3 2.18978
8 1SQL GUN 2.18978
9 6C5F 7L9 2.5641
10 4BMX ADE 2.91971
11 4ASE AV9 2.91971
12 3RWP ABQ 2.91971
13 2VN9 GVD 2.91971
14 1VJE MSE 3.01205
15 2XOC ADP 3.64964
16 5OSW DIU 3.64964
17 6AYU F6P 3.64964
18 1J6X MET 3.64964
19 2RGO FAD 3.64964
20 6G14 G4P 4.37956
21 4U0S ADP 4.37956
22 1SOW NAD 4.37956
23 3GDN HBX 5.10949
24 3GDN FAD 5.10949
25 6BTP E8J 5.10949
26 4XFR CIT 5.83942
27 4J0Q GDP 5.83942
28 1TLG GAL 6.4
29 3AQT RCO 6.53061
30 4CLI 5P8 6.56934
31 4FDU IHS 6.56934
32 1MKY GDP 6.56934
33 4IDT T28 6.56934
34 5NCB JZ3 6.56934
35 4EWH T77 7.29927
36 4FC7 COA 8.0292
37 4FC7 NAP 8.0292
38 2OI2 DP6 8.0292
39 1JXN MFU 8.0292
40 2BWN SIN 8.0292
41 1IZO PAM 8.0292
42 4BCM T7Z 8.0292
43 3FSY SCA 8.75912
44 4Y4V DAL 8.75912
45 5LX9 OLB 8.75912
46 1JAY F42 8.75912
47 3KB6 LAC 9.48905
48 5EW9 5VC 9.48905
49 3SQP 3J8 9.48905
50 1IR3 ANP 9.48905
51 5C9P FUC 10.9489
52 4PZ6 GMP 10.9489
53 4JUI EGR 12.4088
54 1KK1 GNP 13.1387
55 1B4B ARG 15.493
56 4DO1 ANN 20.438
57 5HMC 5NE 35.0365
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