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Receptor
PDB id Resolution Class Description Source Keywords
2EW5 2.2 Å EC: 3.5.1.88 STRUCTURE OF HELICOBACTER PYLORI PEPTIDE DEFORMYLASE IN COMP INHIBITOR HELICOBACTER PYLORI COBALT HELICOBACTER PYLORI PEPTIDE DEFORMYLASE INHIBITOR H
Ref.: PEPTIDE DEFORMYLASE IS A POTENTIAL TARGET FOR ANTI-HELICOBACTER PYLORI DRUGS: REVERSE DOCKING, EN 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 COMP INHIBITOR HELICOBACTER PYLORI COBALT HELICOBACTER PYLORI PEPTIDE DEFORMYLASE INHIBITOR H
Ref.: PEPTIDE DEFORMYLASE IS A POTENTIAL TARGET FOR ANTI-HELICOBACTER PYLORI DRUGS: REVERSE DOCKING, EN 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 (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 1G2A ic50 = 10 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
2 1BS8 - MET ALA SER n/a n/a
3 2AI8 ic50 = 0.16 uM SB7 C10 H15 N O2 c1ccc(cc1)....
4 1G27 ic50 = 7 nM BB1 C16 H31 N3 O4 CCCC[C@H](....
5 1LRU - BB2 C19 H35 N3 O5 CCCCC[C@H]....
6 1BS6 - MET ALA SER n/a n/a
7 2EW6 ic50 = 10.8 uM Y13 C17 H17 N O4 c1cc(ccc1C....
8 2EW5 ic50 = 1.25 uM Y12 C21 H21 N O5 CC(=O)Oc1c....
9 3UWB ic50 = 10 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
10 1RL4 ic50 = 130 nM BL5 C38 H62 N8 O4 CCCC[C@@H]....
11 1S17 ic50 < 5 nM GNR C10 H10 N2 O3 S c1ccc2c(c1....
12 1IX1 - BB2 C19 H35 N3 O5 CCCCC[C@H]....
13 4DR9 ic50 = 10 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
14 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 with APoc: 181
This union binding pocket(no: 1) in the query (biounit: 2ew5.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 1Q3A NGH None
2 1UO4 PIH None
3 1UO5 PIH None
4 2YLD CMO None
5 1RV1 IMZ None
6 4WG0 CHD None
7 5ET3 60C None
8 5TVI MYR None
9 4YV5 SVR None
10 6EVN PRO PRO GLY PRO ALA GLY PRO PRO GLY None
11 3X1M COA None
12 3V78 ET None
13 5TVI O8N None
14 5MWE TCE None
15 5UC9 MYR None
16 5LYH 7B8 None
17 3KV8 FAH None
18 3AQT RCO None
19 2ZX2 RAM 1.10497
20 3R9V DXC 1.10497
21 6F5W KG1 1.10497
22 4WRI OKA 1.10497
23 6H8S FSZ 1.10497
24 4MRP GSH 1.65746
25 3SQP 3J8 1.65746
26 4OGQ 7PH 1.65746
27 4OGQ 1O2 1.65746
28 1UY4 XYP XYP XYP XYP 2.06897
29 6FA4 D1W 2.20994
30 2OZ5 7XY 2.20994
31 3Q2H QHF 2.20994
32 5FH7 5XL 2.41935
33 2FV5 541 2.68199
34 1KUK PCA LYS TRP 2.76243
35 3ROE THM 2.76243
36 2Z9I GLY ALA THR VAL 2.76243
37 1LK7 DER 2.76243
38 1NE7 16G 2.76243
39 3ZXR IQ1 2.76243
40 3ZXR P3S 2.76243
41 5V4R MGT 3.08642
42 6GMN F4E 3.08642
43 5W7B MYR 3.31492
44 4WGF HX2 3.31492
45 1Y7I SAL 3.31492
46 2I3G NAP 3.31492
47 4OEV OXL 3.31492
48 3KVY URA 3.31492
49 1VL1 CIT 3.31492
50 4RDL FUC GAL NDG FUC 3.31492
51 4KJU 1RH 3.48837
52 5Y02 HBX 3.73832
53 5Y02 MXN 3.73832
54 2B56 U5P 3.8674
55 1GJW GLC 3.8674
56 3BJE URA 3.8674
57 5NM7 GLY 3.8674
58 1RQ2 CIT 3.8674
59 4V3I ASP LEU THR ARG PRO 3.8674
60 5N26 CPT 3.8674
61 2W14 WR2 3.8674
62 3ZUY TCH 3.8674
63 4RW3 TDA 3.97351
64 3KP6 SAL 3.97351
65 1XMY ROL 4.0201
66 5OSW DIU 4.41989
67 4ZW3 4S9 4.41989
68 1PNF NDG NAG 4.41989
69 2HZL PYR 4.41989
70 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 4.41989
71 1VA6 ADP 4.41989
72 1VA6 P2S 4.41989
73 1RJW ETF 4.41989
74 1IG0 VIB 4.41989
75 3GD8 GOL 4.41989
76 1OFU GDP 4.6875
77 5H4S RAM 4.97238
78 3E70 GDP 4.97238
79 4FAJ LEU VAL THR LEU VAL PHE VAL 4.97238
80 1U7Z PMT 4.97238
81 3FXU TSU 4.97238
82 1NW4 IMH 4.97238
83 4JWH SAH 4.97238
84 2AK3 AMP 4.97238
85 3ABA FLI 4.97238
86 5X80 SAL 5
87 1GVE NAP 5.50459
88 1ZVX FIN 5.52147
89 1Q7E MET 5.52486
90 5OCG 9R5 5.52486
91 4URX FK1 5.52486
92 5KJW 53C 5.52486
93 1OYF MHN 5.78512
94 1JGS SAL 5.7971
95 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 6.07735
96 2V5E SCR 6.07735
97 4DD8 BAT 6.07735
98 1JN2 SFP 6.07735
99 1O8B ABF 6.07735
100 3ENV ABF 6.07735
101 3LKF PC 6.07735
102 1GPM AMP 6.07735
103 5AB0 2X0 7GA LYS HIS HIS ALA PHE SER PHE LYN 6.07735
104 2YIV YIV 6.62983
105 3B9Z CO2 6.62983
106 1YQS BSA 6.62983
107 5YLF BGC 6.62983
108 5OM2 DXT 6.62983
109 1ATL 0QI 6.62983
110 6BVK EAV 6.62983
111 6BVM EBV 6.62983
112 1ZED PNP 6.62983
113 6BVE PGA 6.62983
114 4WZV E40 6.875
115 3KO0 TFP 6.93069
116 2CJU PHX 7.07965
117 4AIG FLX 7.18232
118 1R6N 434 7.18232
119 2C91 NAP 7.18232
120 2BP1 NDP 7.18232
121 3U1T MLI 7.18232
122 6DQU GLY ILE ILE ASN THR LEU 7.18232
123 1YQT ADP 7.18232
124 4IN9 SER TRP PHE PRO 7.22892
125 3UEC ALA ARG TPO LYS 7.53425
126 1YP1 LYS ASN LEU 7.73481
127 1R55 097 7.73481
128 6BR8 PGV 7.73481
129 5LX9 OLB 7.73481
130 4XNV BUR 7.73481
131 1MMQ RRS 7.73481
132 3VPD CIT 7.73481
133 2YIP YIO 7.97101
134 2D5X L35 8.21918
135 1B7H LYS NLE LYS 8.28729
136 5F1V 3VN 8.28729
137 1TV5 N8E 8.28729
138 2IVN ANP 8.28729
139 3HP9 CF1 8.28729
140 2NVK NAP 8.28729
141 1TV5 A26 8.28729
142 2BVE PH5 8.40336
143 1MID LAP 8.79121
144 5C1M OLC 8.83978
145 4WKI 3PW 8.83978
146 3X01 AMP 8.83978
147 5OLK DTP 8.83978
148 3G58 988 8.83978
149 4F4S EFO 9.21053
150 2J83 BAT 9.39227
151 1FBL HTA 9.39227
152 3ZVS MLI 9.39227
153 4DPL NAP 9.39227
154 3BJC WAN 9.39227
155 4LO6 SIA GAL 9.39227
156 1T3D CYS 9.94475
157 4EOY ASN ASP TRP LEU LEU PRO SER TYR 10.1562
158 2Q8G AZX 10.4972
159 5C9J DAO 11.1111
160 5WL1 D3D 11.1111
161 2Y69 CHD 11.1111
162 3GUZ PAF 11.9318
163 4UCC ZKW 12.1547
164 1M2Z BOG 12.7072
165 2GWH PCI 12.7517
166 5TCI MLI 13.2597
167 4MGA 27L 13.2597
168 2JC9 ADN 13.2597
169 4TV1 36M 13.2597
170 3LXI CAM 13.8122
171 3QPB URA 13.8122
172 5YV5 ADP 14.3646
173 5W97 CHD 14.8936
174 3W54 RNB 14.9171
175 5L7G LYS SER LEU LEU GLN GLN LEU LEU THR GLU 16.0221
176 4GK9 MAN BMA MAN MAN MAN 16.0221
177 3H0L ADP 17.0213
178 1LNX URI 18.5185
179 3WV1 WHH 19.2982
180 4JTA NAP 21.6216
181 3C3N FMN 23.7569
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