Receptor
PDB id Resolution Class Description Source Keywords
2EW5 2.2 Å EC: 3.5.1.88 STRUCTURE OF HELICOBACTER PYLORI PEPTIDE DEFORMYLASE IN COMPLEX WITH INHIBITOR HELICOBACTER PYLORI COBALT HELICOBACTER PYLORI PEPTIDE DEFORMYLASE INHIBITOR HYDROLASE
Ref.: PEPTIDE DEFORMYLASE IS A POTENTIAL TARGET FOR ANTI-HELICOBACTER PYLORI DRUGS: REVERSE DOCKING, ENZYMATIC ASSAY, AND X-RAY CRYSTALLOGRAPHY VALIDATION PROTEIN SCI. V. 15 2071 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CO A:300;
Part of Protein;
none;
submit data
58.933 Co [Co+2...
Y12 A:200;
Valid;
none;
ic50 = 1.25 uM
367.395 C21 H21 N O5 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2EW5 2.2 Å EC: 3.5.1.88 STRUCTURE OF HELICOBACTER PYLORI PEPTIDE DEFORMYLASE IN COMPLEX WITH INHIBITOR HELICOBACTER PYLORI COBALT HELICOBACTER PYLORI PEPTIDE DEFORMYLASE INHIBITOR HYDROLASE
Ref.: PEPTIDE DEFORMYLASE IS A POTENTIAL TARGET FOR ANTI-HELICOBACTER PYLORI DRUGS: REVERSE DOCKING, ENZYMATIC ASSAY, AND X-RAY CRYSTALLOGRAPHY VALIDATION PROTEIN SCI. V. 15 2071 2006
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 2EW6 ic50 = 10.8 uM Y13 C17 H17 N O4 c1cc(ccc1C....
2 2EW5 ic50 = 1.25 uM Y12 C21 H21 N O5 CC(=O)Oc1c....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 2EW6 ic50 = 10.8 uM Y13 C17 H17 N O4 c1cc(ccc1C....
2 2EW5 ic50 = 1.25 uM Y12 C21 H21 N O5 CC(=O)Oc1c....
50% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 1WS1 Ki = 0.28 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
2 1G2A ic50 = 10 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
3 1BS8 - MET ALA SER n/a n/a
4 2AI8 ic50 = 0.16 uM SB7 C10 H15 N O2 c1ccc(cc1)....
5 1G27 ic50 = 7 nM BB1 C16 H31 N3 O4 CCCC[C@H](....
6 1LRU - BB2 C19 H35 N3 O5 CCCCC[C@H]....
7 1BS6 - MET ALA SER n/a n/a
8 2EW6 ic50 = 10.8 uM Y13 C17 H17 N O4 c1cc(ccc1C....
9 2EW5 ic50 = 1.25 uM Y12 C21 H21 N O5 CC(=O)Oc1c....
10 3UWB ic50 = 10 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
11 1RL4 ic50 = 130 nM BL5 C38 H62 N8 O4 CCCC[C@@H]....
12 1S17 ic50 < 5 nM GNR C10 H10 N2 O3 S c1ccc2c(c1....
13 1IX1 - BB2 C19 H35 N3 O5 CCCCC[C@H]....
14 4DR9 ic50 = 10 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
15 3M6P Kd = 0.9 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
16 3M6R Kd = 32 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
17 3M6Q Kd = 48 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: Y12; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 Y12 1 1
2 Y13 0.417722 0.809524
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2EW5; Ligand: Y12; Similar sites found: 93
This union binding pocket(no: 1) in the query (biounit: 2ew5.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1Q3A NGH 0.0004961 0.48081 None
2 1UO4 PIH 0.001639 0.47141 None
3 1UO5 PIH 0.005644 0.46438 None
4 2YLD CMO 0.003253 0.45305 None
5 3V78 ET 0.007065 0.41489 None
6 5TVI MYR 0.01435 0.41217 None
7 5TVI O8N 0.02631 0.40613 None
8 5MWE TCE 0.02129 0.40412 None
9 5UC9 MYR 0.01775 0.40383 None
10 4WG0 CHD 0.02965 0.40148 None
11 3AQT RCO 0.03154 0.40008 None
12 2ZX2 RAM 0.003443 0.4524 1.10497
13 4MRP GSH 0.004463 0.44504 1.65746
14 3SQP 3J8 0.007737 0.43156 1.65746
15 1UY4 XYP XYP XYP XYP 0.0183 0.41058 2.06897
16 3Q2H QHF 0.004505 0.40839 2.20994
17 5FH7 5XL 0.01406 0.40887 2.41935
18 1KUK PCA LYS TRP 0.00004953 0.51621 2.76243
19 2Z9I GLY ALA THR VAL 0.02114 0.40908 2.76243
20 5V4R MGT 0.006589 0.441 3.08642
21 4OEV OXL 0.02395 0.40466 3.31492
22 1VL1 CIT 0.02852 0.40168 3.31492
23 4RDL FUC GAL NDG FUC 0.0256 0.4012 3.31492
24 4KJU 1RH 0.01002 0.42116 3.48837
25 1GJW GLC 0.01105 0.41706 3.8674
26 1SW0 PGA 0.006764 0.41578 3.8674
27 4V3I ASP LEU THR ARG PRO 0.02418 0.40626 3.8674
28 2W14 WR2 0.0111 0.40181 3.8674
29 4RW3 TDA 0.007267 0.44332 3.97351
30 3KP6 SAL 0.005621 0.44026 3.97351
31 1XMY ROL 0.01109 0.41401 4.0201
32 1PNF NDG NAG 0.01278 0.41768 4.41989
33 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 0.01655 0.41693 4.41989
34 2WZ5 MET 0.007008 0.43535 4.57516
35 3HY9 098 0.002376 0.42033 4.97238
36 1NW4 IMH 0.01779 0.40379 4.97238
37 2AK3 AMP 0.02711 0.40036 4.97238
38 5X80 SAL 0.02682 0.40554 5
39 4URX FK1 0.01672 0.42714 5.52486
40 4DSU BZI 0.01283 0.40955 5.52486
41 5KJW 53C 0.02063 0.40669 5.52486
42 1OYF MHN 0.01468 0.41169 5.78512
43 1JGS SAL 0.0001528 0.51112 5.7971
44 2V5E SCR 0.00284 0.46527 6.07735
45 4DD8 BAT 0.001423 0.46397 6.07735
46 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 0.008798 0.43209 6.07735
47 1O8B ABF 0.007592 0.42218 6.07735
48 1QDS PGA 0.01166 0.40864 6.07735
49 3LKF PC 0.02654 0.40812 6.07735
50 1GPM AMP 0.02393 0.40137 6.07735
51 2YIV YIV 0.003052 0.4606 6.62983
52 3B9Z CO2 0.004056 0.45761 6.62983
53 1ATL 0QI 0.001321 0.41211 6.62983
54 3KO0 TFP 0.02525 0.40035 6.93069
55 2CJU PHX 0.02428 0.40128 7.07965
56 4AIG FLX 0.00006907 0.51606 7.18232
57 3U1T MLI 0.008885 0.42778 7.18232
58 4IN9 SER TRP PHE PRO 0.004334 0.44434 7.22892
59 3UEC ALA ARG TPO LYS 0.00201 0.45562 7.53425
60 1YP1 LYS ASN LEU 0.001794 0.45887 7.73481
61 1R55 097 0.003484 0.43893 7.73481
62 4XNV BUR 0.006697 0.42714 7.73481
63 1MMQ RRS 0.002285 0.42497 7.73481
64 3VPD CIT 0.006955 0.41289 7.73481
65 2YIP YIO 0.005659 0.43784 7.97101
66 1RM8 BAT 0.003233 0.44587 8.28402
67 1TV5 N8E 0.01752 0.42057 8.28729
68 3HP9 CF1 0.02472 0.40431 8.28729
69 2NVK NAP 0.0216 0.4038 8.28729
70 1TV5 A26 0.01557 0.40255 8.28729
71 2BVE PH5 0.01312 0.40974 8.40336
72 5C1M OLC 0.002108 0.46538 8.83978
73 4WKI 3PW 0.003982 0.42663 8.83978
74 3G58 988 0.01341 0.4057 8.83978
75 4F4S EFO 0.02199 0.4034 9.21053
76 1FBL HTA 0.001234 0.45574 9.39227
77 2J83 BAT 0.0002383 0.45559 9.39227
78 3ZVS MLI 0.01564 0.41098 9.39227
79 3BJC WAN 0.02333 0.40208 9.39227
80 4LO6 SIA GAL 0.02154 0.40007 9.39227
81 1T3D CYS 0.02046 0.40457 9.94475
82 4EOY ASN ASP TRP LEU LEU PRO SER TYR 0.01717 0.40048 10.1562
83 2Y69 CHD 0.01445 0.41467 11.1111
84 4UCC ZKW 0.0107 0.42861 12.1547
85 1M2Z BOG 0.01104 0.41282 12.7072
86 5TCI MLI 0.004821 0.43323 13.2597
87 3LXI CAM 0.003852 0.44358 13.8122
88 3QPB URA 0.01424 0.41164 13.8122
89 5W97 CHD 0.02108 0.40625 14.8936
90 3W54 RNB 0.01061 0.40272 14.9171
91 5L7G LYS SER LEU LEU GLN GLN LEU LEU THR GLU 0.005165 0.43047 16.0221
92 4GK9 MAN BMA MAN MAN MAN 0.02509 0.40333 16.0221
93 3H0L ADP 0.0006843 0.4739 17.0213
Feedback