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Receptor
PDB id Resolution Class Description Source Keywords
3SVJ 1.55 Å EC: 3.5.1.88 STREP PEPTIDE DEFORMYLASE WITH A TIME DEPENDENT THIAZOLIDINE STREPTOCOCCUS PNEUMONIAE ALPHA-BETA PEPTIDE DEFORMYLASE METAL BINDING PROTEIN HYDRHYDROLASE INHIBITOR COMPLEX
Ref.: UNDERSTANDING THE ORIGINS OF TIME-DEPENDENT INHIBIT POLYPEPTIDE DEFORMYLASE INHIBITORS. BIOCHEMISTRY V. 50 6642 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
4LI P:207;
Valid;
none;
Ki = 117 nM
582.12 C27 H32 Cl N9 O2 S Cc1cc...
GOL P:209;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NI P:208;
Part of Protein;
none;
submit data
58.693 Ni [Ni+2...
SO4 P:204;
P:205;
P:206;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4EOX 1.78 Å EC: 3.5.1.88 X-RAY STRUCTURE OF POLYPEPTIDE DEFORMYLASE BOUND TO A ACYLPR INHIBITOR STREPTOCOCCUS PNEUMONIAE ALPHA-BETA PEPTIDE DEFORMYLASE METAL ION BINDING HYDROLASEHYDROLASE INHIBITOR COMPLEX
Ref.: ACYLPROLINAMIDES: A NEW CLASS OF PEPTIDE DEFORMYLAS INHIBITORS WITH IN VIVO ANTIBACTERIAL ACTIVITY. BIOORG.MED.CHEM.LETT. V. 22 4028 2012
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 3SW8 Ki = 25910 nM 5LI C10 H10 Cl2 N2 O3 c1cc(c(c(c....
2 3SVJ Ki = 117 nM 4LI C27 H32 Cl N9 O2 S Cc1cccc(c1....
3 2AI7 ic50 = 0.4 uM SB7 C10 H15 N O2 c1ccc(cc1)....
4 2AIE ic50 = 2.2 uM SB9 C10 H14 N2 O2 Cc1cccc(n1....
5 2AIA ic50 = 3.9 uM SB8 C16 H15 N O4 c1ccc(cc1)....
6 4EOX ic50 = 0.28 nM 0S5 C22 H29 N3 O5 c1ccc(cc1)....
7 3STR Ki = 334 nM 3LI C28 H33 Cl N10 O4 S Cc1cccc(c1....
70% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 3SW8 Ki = 25910 nM 5LI C10 H10 Cl2 N2 O3 c1cc(c(c(c....
2 3SVJ Ki = 117 nM 4LI C27 H32 Cl N9 O2 S Cc1cccc(c1....
3 2AI7 ic50 = 0.4 uM SB7 C10 H15 N O2 c1ccc(cc1)....
4 2AIE ic50 = 2.2 uM SB9 C10 H14 N2 O2 Cc1cccc(n1....
5 2AIA ic50 = 3.9 uM SB8 C16 H15 N O4 c1ccc(cc1)....
6 4EOX ic50 = 0.28 nM 0S5 C22 H29 N3 O5 c1ccc(cc1)....
7 3STR Ki = 334 nM 3LI C28 H33 Cl N10 O4 S Cc1cccc(c1....
8 3G6N - MET ALA SER n/a n/a
9 2OKL - BB2 C19 H35 N3 O5 CCCCC[C@H]....
10 1LQY - BB2 C19 H35 N3 O5 CCCCC[C@H]....
11 5JF3 Ki = 38 nM SF5 C18 H23 N3 O5 CCCC[C@H](....
12 5JEZ - MET ALA SER n/a n/a
13 5JF7 Ki = 909 nM 6JU C17 H15 Br N2 O2 c1ccc(cc1)....
14 5JF2 Ki = 13 nM SF7 C16 H20 F N3 O3 CCCC[C@H](....
15 5JF5 Ki = 63 nM 7JT C19 H23 N3 O5 c1cc2c(cc1....
16 5JF0 - MET ALA ARG n/a n/a
17 5JF4 Ki = 65 nM 6JT C20 H23 N3 O4 c1ccc2c(c1....
18 5JF6 Ki = 62 nM BB4 C10 H9 Br N2 O2 c1cc2c(cc1....
19 5JF1 Ki = 64 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
20 5JF8 Ki = 1428 nM PN3 C15 H22 N2 O4 CC(C)(C)OC....
50% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3SW8 Ki = 25910 nM 5LI C10 H10 Cl2 N2 O3 c1cc(c(c(c....
2 3SVJ Ki = 117 nM 4LI C27 H32 Cl N9 O2 S Cc1cccc(c1....
3 2AI7 ic50 = 0.4 uM SB7 C10 H15 N O2 c1ccc(cc1)....
4 2AIE ic50 = 2.2 uM SB9 C10 H14 N2 O2 Cc1cccc(n1....
5 2AIA ic50 = 3.9 uM SB8 C16 H15 N O4 c1ccc(cc1)....
6 4EOX ic50 = 0.28 nM 0S5 C22 H29 N3 O5 c1ccc(cc1)....
7 3STR Ki = 334 nM 3LI C28 H33 Cl N10 O4 S Cc1cccc(c1....
8 3G6N - MET ALA SER n/a n/a
9 2OKL - BB2 C19 H35 N3 O5 CCCCC[C@H]....
10 1Q1Y - BB2 C19 H35 N3 O5 CCCCC[C@H]....
11 1LQY - BB2 C19 H35 N3 O5 CCCCC[C@H]....
12 5JF3 Ki = 38 nM SF5 C18 H23 N3 O5 CCCC[C@H](....
13 5JEZ - MET ALA SER n/a n/a
14 5JF7 Ki = 909 nM 6JU C17 H15 Br N2 O2 c1ccc(cc1)....
15 5JF2 Ki = 13 nM SF7 C16 H20 F N3 O3 CCCC[C@H](....
16 5JF5 Ki = 63 nM 7JT C19 H23 N3 O5 c1cc2c(cc1....
17 5JF0 - MET ALA ARG n/a n/a
18 5JF4 Ki = 65 nM 6JT C20 H23 N3 O4 c1ccc2c(c1....
19 5JF6 Ki = 62 nM BB4 C10 H9 Br N2 O2 c1cc2c(cc1....
20 5JF1 Ki = 64 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
21 5JF8 Ki = 1428 nM PN3 C15 H22 N2 O4 CC(C)(C)OC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 4LI; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 4LI 1 1
2 3LI 0.816514 0.821429
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4EOX; Ligand: 0S5; Similar sites found with APoc: 213
This union binding pocket(no: 1) in the query (biounit: 4eox.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 5UGW GSH None
2 1HBK COA None
3 5C2N NAG None
4 1J1R ADE None
5 4WG0 CHD None
6 5NNT DPV None
7 1ZEI CRS None
8 3GKJ HC3 None
9 5C9P FUC 0.985222
10 3UYW TAU 0.985222
11 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 1.47783
12 1YP1 LYS ASN LEU 1.48515
13 5N26 CPT 1.64835
14 2O5L MNR 1.96078
15 1KUK PCA LYS TRP 1.97044
16 3HP9 CF1 1.97044
17 3R9V DXC 1.97044
18 4GK9 MAN BMA MAN MAN MAN 1.97044
19 1SBR VIB 2
20 1BWO LPC 2.22222
21 1NX0 ALA LYS ALA ILE ALA 2.31214
22 4RW3 TDA 2.46305
23 2B56 U5P 2.46305
24 5HCN DAO 2.46305
25 6C1R EFD 2.46305
26 5WBF LAC 2.46305
27 4I90 CHT 2.46305
28 4LEB THR THR THR THR THR THR THR 2.46305
29 1UI0 URA 2.46305
30 3AQT RCO 2.46305
31 2OUA AES 2.65957
32 5CHR 4NC 2.91971
33 1MMQ RRS 2.94118
34 4GAA BES 2.95567
35 2XQ0 BES 2.95567
36 3G58 988 2.95567
37 6H8S FSZ 2.95567
38 6BMN PAP 2.95567
39 3WLV AZA 2.95567
40 2HZL PYR 2.95567
41 5O7E 9NB 2.95567
42 5IM3 DTP 2.95567
43 2V5E SCR 3
44 4B6C B5U 3.06122
45 4DS0 A2G GAL NAG FUC 3.06748
46 5V4R MGT 3.08642
47 3SJK LYS PRO VAL LEU ARG THR ALA 3.15789
48 4P8O 883 3.20856
49 3NFD COA 3.26797
50 1MID LAP 3.2967
51 3KCG NTP 3.38983
52 4WKI 3PW 3.44828
53 1BKC INN 3.44828
54 2YFB SIN 3.44828
55 2FV5 541 3.44828
56 1OFZ FUC 3.44828
57 1XMY ROL 3.44828
58 4V3I ASP LEU THR ARG PRO 3.44828
59 1YXM ADE 3.44828
60 1XM4 PIL 3.44828
61 5Z3I ADE 3.44828
62 4UCC ZKW 3.44828
63 1TL2 NDG 3.44828
64 2YB9 HA0 3.44828
65 3WV1 WHH 3.50877
66 1RM8 BAT 3.5503
67 5CSD ACD 3.77358
68 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 3.94089
69 5NC1 NAG 3.94089
70 1ZPD CIT 3.94089
71 1TE2 PGA 3.94089
72 4MRP GSH 3.94089
73 4AG5 ADP 3.94089
74 5UC9 MYR 3.94089
75 4BXK 1IU 3.94089
76 2UW1 GVM 3.94089
77 1VAY AZA 3.94089
78 1XF1 CIT 3.94089
79 1PCA CIT 3.94089
80 5AZC PGT 4
81 5TVI O8N 4.34783
82 3ZVS MLI 4.375
83 4WZV E40 4.375
84 1R55 097 4.4335
85 4AR8 IP8 GLY PRO ALA 4.4335
86 4KX8 L2O VAL VAL ASP 4.4335
87 5FPN KYD 4.4335
88 5CX6 CDP 4.4335
89 2V57 PRL 4.73684
90 4DV8 0LX 4.92611
91 4ZW3 4S9 4.92611
92 1ZED PNP 4.92611
93 3E70 GDP 4.92611
94 4UMJ BFQ 4.92611
95 3CHT 4NB 4.92611
96 5AB0 2X0 7GA LYS HIS HIS ALA PHE SER PHE LYN 4.92611
97 1UOU CMU 4.92611
98 2ZXG S23 4.92611
99 2Q8G AZX 4.92611
100 2W14 WR2 4.9505
101 3SQP 3J8 5.02092
102 2WMC MGP 5.05618
103 1GNY XYP XYP XYP XYP XYP 5.22876
104 3KP6 SAL 5.29801
105 4DD8 BAT 5.41872
106 3HBV ALA LYS ALA SER GLN ALA ALA 5.41872
107 5EXA 5SO 5.41872
108 2WPF FAD 5.41872
109 3SDV 911 5.41872
110 3GXO MQA 5.41872
111 5KAU RHQ 5.45455
112 2GBB CIT 5.76923
113 6GMN F4E 5.76923
114 1UO4 PIH 5.88235
115 3W5N RAM 5.91133
116 1R6N 434 5.91133
117 2IDO TMP 5.91398
118 3KO0 TFP 5.94059
119 6BTN E8M 5.94059
120 1NU4 MLA 6.18557
121 4F8L AES 6.2069
122 3Q2H QHF 6.40394
123 4B52 RDF 6.40394
124 5DT6 GLU 6.40394
125 3KIF GDL 6.60377
126 5OCG 9R5 6.87831
127 2J83 BAT 6.89655
128 4WGF HX2 6.89655
129 5TVA AMP 6.89655
130 4LBP 1WG 7
131 6HT0 GQ8 7.09677
132 6CWH 6LA 7.14286
133 3KIH GDL 7.2165
134 3NJQ NJQ 7.25389
135 6MJ7 ARG 7.27273
136 2GWH PCI 7.38916
137 5C9J DAO 7.38916
138 5OSW DIU 7.38916
139 5OCA 9QZ 7.38916
140 5ECP ATP 7.38916
141 5ECP JAA 7.38916
142 5ECP MET 7.38916
143 1GET NAP 7.38916
144 1GET FAD 7.38916
145 3ROE THM 7.38916
146 1SJD NPG 7.38916
147 4AIG FLX 7.46269
148 3UEC ALA ARG TPO LYS 7.53425
149 4RJD TFP 7.57576
150 3DWB RDF 7.88177
151 1ZVX FIN 7.97546
152 5X13 HC4 7.97872
153 6FA4 D1W 8.09249
154 2XYA 7L4 8.24176
155 1FBL HTA 8.37438
156 3O01 DXC 8.37438
157 2ZWI C5P 8.37438
158 4C2C ALA ALA ALA 8.37438
159 5Y02 HBX 8.41121
160 2P0D I3P 8.52713
161 5LX9 OLB 8.86699
162 5ZRR 9J3 8.86699
163 5V3Y 5V8 8.86699
164 5C1M OLC 9.12162
165 5KDS A2G THR ALA PRO GLY GLY NAG SIA 9.35961
166 1IXI 2HP 9.35961
167 4ZGM 32M 9.83607
168 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 9.85222
169 1ATL 0QI 9.90099
170 2TCL RO4 10.0592
171 4IN9 SER TRP PHE PRO 10.241
172 1SQL GUN 10.274
173 1RZM E4P 10.3448
174 1ZGA HMK 10.3448
175 2VJ8 HA2 10.8374
176 2VWA PTY 10.8911
177 4K91 SIN 11.33
178 4QOM PYG 11.8227
179 6BR8 PGV 11.8227
180 6BVM EBV 11.8227
181 5G5G MCN 12.3153
182 1N8V BDD 12.5
183 1HFS L04 13.125
184 1Q3A NGH 13.3333
185 3N7S 3N7 13.5417
186 4F4S EFO 14.4737
187 1T0S BML 15.1163
188 4CA5 3EF 15.2709
189 5FQK 6NT 15.9851
190 5ZI7 GLU 16.2562
191 3X01 AMP 16.7488
192 5LWY OLB 16.8224
193 4OGQ 2WD 17.5
194 4OGQ 1O2 17.5
195 4OGQ 7PH 17.5
196 2Z9I GLY ALA THR VAL 17.5926
197 5KD8 TNR 17.734
198 3ETG GTP 20.6897
199 5Z84 CHD 21.4286
200 5ZCO CHD 21.4286
201 5W97 CHD 21.4286
202 2Y69 CHD 21.7054
203 2QQD AG2 22.6415
204 1ELW GLY PRO THR ILE GLU GLU VAL ASP 22.8814
205 1MT1 AG2 23.0769
206 3V78 ET 23.6453
207 3RLF MAL 24.6305
208 5A86 D7E 29.4118
209 5M36 9SZ 31.5789
210 4TV1 36M 38.4615
211 4MGA 27L 38.4615
212 1G27 BB1 38.6905
213 1RL4 BRR 49.4681
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