-->
Receptor
PDB id Resolution Class Description Source Keywords
5JF2 2 Å EC: 3.5.1.88 CRYSTAL STRUCTURE OF TYPE 2 PDF FROM STREPTOCOCCUS AGALACTIA COMPLEX WITH INHIBITOR AT002 STREPTOCOCCUS AGALACTIAE PDF TYPE 2 NME N-TERMINAL METHIONINE EXCISION STREPTOCOCAGALACTIAE INHIBITOR AT002 HYDROLASE
Ref.: A UNIQUE PEPTIDE DEFORMYLASE PLATFORM TO RATIONALLY AND CHALLENGE NOVEL ACTIVE COMPOUNDS. SCI REP V. 6 35429 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN A:310;
A:308;
A:306;
A:311;
A:307;
A:304;
A:305;
A:309;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
IMD A:303;
Invalid;
none;
submit data
69.085 C3 H5 N2 c1c[n...
ACT A:302;
Invalid;
none;
submit data
59.044 C2 H3 O2 CC(=O...
SF7 A:301;
Valid;
Atoms found LESS than expected: % Diff = 0;
Ki = 13 nM
321.347 C16 H20 F N3 O3 CCCC[...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5JF2 2 Å EC: 3.5.1.88 CRYSTAL STRUCTURE OF TYPE 2 PDF FROM STREPTOCOCCUS AGALACTIA COMPLEX WITH INHIBITOR AT002 STREPTOCOCCUS AGALACTIAE PDF TYPE 2 NME N-TERMINAL METHIONINE EXCISION STREPTOCOCAGALACTIAE INHIBITOR AT002 HYDROLASE
Ref.: A UNIQUE PEPTIDE DEFORMYLASE PLATFORM TO RATIONALLY AND CHALLENGE NOVEL ACTIVE COMPOUNDS. SCI REP V. 6 35429 2016
Members (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 5JF3 Ki = 38 nM SF5 C18 H23 N3 O5 CCCC[C@H](....
2 5JEZ - MET ALA SER n/a n/a
3 5JF7 Ki = 909 nM 6JU C17 H15 Br N2 O2 c1ccc(cc1)....
4 5JF2 Ki = 13 nM SF7 C16 H20 F N3 O3 CCCC[C@H](....
5 5JF5 Ki = 63 nM 7JT C19 H23 N3 O5 c1cc2c(cc1....
6 5JF0 - MET ALA ARG n/a n/a
7 5JF4 Ki = 65 nM 6JT C20 H23 N3 O4 c1ccc2c(c1....
8 5JF6 Ki = 62 nM BB4 C10 H9 Br N2 O2 c1cc2c(cc1....
9 5JF1 Ki = 64 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
10 5JF8 Ki = 1428 nM PN3 C15 H22 N2 O4 CC(C)(C)OC....
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: SF7; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 SF7 1 1
2 SF5 0.736842 0.835821
3 7JT 0.40404 0.742857
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5JF2; Ligand: SF7; Similar sites found with APoc: 213
This union binding pocket(no: 1) in the query (biounit: 5jf2.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 4WGF HX2 None
2 4LBP 1WG None
3 4M8X KGQ None
4 2O4N TPV None
5 4WG0 CHD None
6 2QZT PLM None
7 3GGU 017 None
8 5UC9 MYR None
9 1HBK COA None
10 4XCP PLM None
11 5C2N NAG None
12 3AQT RCO None
13 5NNT DPV None
14 6C8X BVR None
15 3U7S 017 None
16 3KA2 2NC None
17 1UKG MMA 1.5873
18 6FA4 D1W 1.7341
19 3NJQ NJQ 2.07254
20 5CHR 4NC 2.18978
21 5N26 CPT 2.1978
22 1BWO LPC 2.22222
23 4RW3 TDA 2.45098
24 1XMY ROL 2.45098
25 3G58 988 2.45098
26 1XM4 PIL 2.45098
27 1XMU ROF 2.45098
28 5FUS DAO 2.45098
29 3GKJ HC3 2.45098
30 5OHJ 9VE 2.45098
31 1XON PIL 2.45098
32 6ARJ SAH 2.45098
33 6ARJ BW4 2.45098
34 1KUK PCA LYS TRP 2.46305
35 1OYF MHN 2.47934
36 5XNA SHV 2.89855
37 4WKI 3PW 2.94118
38 1MMQ RRS 2.94118
39 2ZXG S23 2.94118
40 2XQ0 BES 2.94118
41 2Z48 NGA 2.94118
42 5O7E 9NB 2.94118
43 5NC1 NAG 2.94118
44 2Z49 AMG 2.94118
45 4GAA BES 2.94118
46 6H8S FSZ 2.94118
47 4MGA 27L 2.94118
48 3GZ9 D32 2.94118
49 1Y7I SAL 2.94118
50 4RFM 3P6 2.94118
51 4MG9 27K 2.94118
52 2X5W K2B 2.94118
53 1YP1 LYS ASN LEU 2.9703
54 2W14 WR2 2.9703
55 1MID LAP 3.2967
56 3KP6 SAL 3.31126
57 1BKC INN 3.43137
58 4MRP GSH 3.43137
59 2VJ8 HA2 3.43137
60 2FV5 541 3.43137
61 4KX8 L2O VAL VAL ASP 3.43137
62 5AZC PGT 3.43137
63 2YB9 HA0 3.43137
64 3KRO DST 3.43137
65 3KRO IPE 3.43137
66 4QOM PYG 3.43137
67 4AR8 IP8 GLY PRO ALA 3.43137
68 3SQP 3J8 3.43137
69 5IUY BOG 3.43137
70 2HZL PYR 3.43137
71 1TL2 NDG 3.43137
72 4AIG FLX 3.48259
73 2V5E SCR 3.5
74 2TCL RO4 3.5503
75 5CSD ACD 3.77358
76 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 3.92157
77 2YFB SIN 3.92157
78 3B9Z CO2 3.92157
79 1A5Z FBP 3.92157
80 3NFD COA 3.92157
81 6BVK EAV 3.92157
82 6BVM EBV 3.92157
83 4URX FK1 3.92157
84 6BVJ EAS 3.92157
85 5F1R 42O 3.92157
86 4Q5M ROC 3.94089
87 3ZVS MLI 4.375
88 1R55 097 4.41176
89 3KCG NTP 4.41176
90 5Z49 RUB 4.41176
91 2ZCQ B65 4.41176
92 4F06 PHB 4.41176
93 3VPD CIT 4.41176
94 3ETG GTP 4.41176
95 3ROE THM 4.41176
96 1ATL 0QI 4.45545
97 5UGW GSH 4.57143
98 3R1V AZB 4.72441
99 2V57 PRL 4.73684
100 4IN9 SER TRP PHE PRO 4.81928
101 1Q3A NGH 4.84848
102 2GWH PCI 4.90196
103 3CHT 4NB 4.90196
104 2YIV YIV 4.90196
105 4K90 MLA 4.90196
106 6CWH 6LA 4.94506
107 1HFS L04 5
108 4WZV E40 5
109 1RM8 BAT 5.32544
110 4DD8 BAT 5.39216
111 3O01 DXC 5.39216
112 1R6N 434 5.39216
113 3DWB RDF 5.39216
114 5HCN DAO 5.39216
115 4Y9J UCC 5.39216
116 4XU6 TDA 5.39216
117 4GK9 MAN BMA MAN MAN MAN 5.39216
118 4UMJ BFQ 5.39216
119 4B52 RDF 5.39216
120 5IM3 DTP 5.39216
121 5TVI O8N 5.43478
122 5TVI MYR 5.43478
123 2D5X L35 5.47945
124 2GBB CIT 5.76923
125 5C9J DAO 5.88235
126 3E70 GDP 5.88235
127 3X01 AMP 5.88235
128 1UOU CMU 5.88235
129 1RQJ RIS 5.88235
130 5FQK 6NT 5.88235
131 3LZW NAP 5.88235
132 1IDA 0PO 6.06061
133 4RJD TFP 6.06061
134 4MA6 28E 6.36943
135 2Q8G AZX 6.37255
136 4PGK Y69 6.37255
137 3Q2H QHF 6.86275
138 4DV8 0LX 6.86275
139 5OSW DIU 6.86275
140 5AB0 2X0 7GA LYS HIS HIS ALA PHE SER PHE LYN 6.86275
141 4BXK 1IU 6.86275
142 5LX9 OLB 6.86275
143 4V3I ASP LEU THR ARG PRO 6.86275
144 5OCA 9QZ 6.86275
145 3RLF MAL 6.86275
146 4NJS G08 7.07071
147 5T2Z 017 7.07071
148 6HT0 GQ8 7.09677
149 1NU4 MLA 7.2165
150 5IKH 6BW 7.35294
151 2BCG GER 7.35294
152 5EK3 5PK 7.35294
153 5Z3I ADE 7.35294
154 5V4R MGT 7.40741
155 5Y02 HBX 7.47664
156 5Y02 MXN 7.47664
157 6GMN F4E 7.69231
158 5W7B MYR 7.80142
159 4CA5 3EF 7.84314
160 3HP9 CF1 7.84314
161 3W5N RAM 7.84314
162 3C88 ARG ARG GLY CYS NH2 7.84314
163 1ZVX FIN 7.97546
164 2Z9I GLY ALA THR VAL 8.33333
165 1ZED PNP 8.33333
166 3R9V DXC 8.33333
167 5WL1 CUY 8.33333
168 2ZWI C5P 8.33333
169 6BTN E8M 8.41584
170 4O4Z N2O 8.44156
171 5X13 HC4 8.51064
172 1ZPD CIT 8.82353
173 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 8.82353
174 1XF1 CIT 8.82353
175 5KAU RHQ 9.09091
176 4UCC ZKW 9.31373
177 5CX6 CDP 9.31373
178 2OUA AES 9.57447
179 5C1M OLC 9.6
180 4B6C B5U 9.69388
181 2J83 BAT 10.2941
182 5M36 9SZ 10.5263
183 2VWA PTY 10.8911
184 3WV1 WHH 11.1111
185 3RV5 DXC 11.236
186 3V66 D3A 11.2745
187 6BR8 PGV 12.2549
188 4ZW3 4S9 12.7451
189 5LWY OLB 13.0841
190 5KDS A2G THR ALA PRO GLY GLY NAG SIA 13.2353
191 3N7S 3N7 13.5417
192 3KO0 TFP 13.8614
193 1FBL HTA 14.7059
194 2Y69 CHD 14.7287
195 1N8V BDD 15.1786
196 5KD8 TNR 17.6471
197 3HBV ALA LYS ALA SER GLN ALA ALA 18.1373
198 1UI0 URA 20.5882
199 3QLM PLM 21.7742
200 4F4S EFO 25
201 3RMK BML 26.506
202 5Z84 CHD 26.5306
203 5ZCO CHD 26.5306
204 5ZCO PGV 26.5306
205 5Z84 PGV 26.5306
206 2DYR PGV 26.5306
207 5W97 CHD 26.5306
208 1T0S BML 27.907
209 4OGQ 2WD 35.1351
210 4OGQ 7PH 35.1351
211 4OGQ 1O2 35.1351
212 1G27 BB1 38.0952
213 1RL4 BRR 49.4681
APoc FAQ
Feedback