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Receptor
PDB id Resolution Class Description Source Keywords
2OKL 1.7 Å EC: 3.5.1.88 CRYSTAL STRUCTURE OF PEPTIDE DEFORMYLASE 2 WITH ACTINONIN FR BACILLUS CEREUS BACILLUS CEREUS HYDROLASE
Ref.: CHARACTERIZATION OF PEPTIDE DEFORMYLASE2 FROM B. CE J.BIOCHEM.MOL.BIOL. V. 40 1050 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BB2 A:401;
A:404;
B:402;
B:403;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
385.498 C19 H35 N3 O5 CCCCC...
CIT A:501;
Invalid;
none;
submit data
192.124 C6 H8 O7 C(C(=...
ZN A:601;
B:602;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2OKL 1.7 Å EC: 3.5.1.88 CRYSTAL STRUCTURE OF PEPTIDE DEFORMYLASE 2 WITH ACTINONIN FR BACILLUS CEREUS BACILLUS CEREUS HYDROLASE
Ref.: CHARACTERIZATION OF PEPTIDE DEFORMYLASE2 FROM B. CE J.BIOCHEM.MOL.BIOL. V. 40 1050 2007
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 2OKL - BB2 C19 H35 N3 O5 CCCCC[C@H]....
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: BB2; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 BB2 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2OKL; Ligand: BB2; Similar sites found with APoc: 270
This union binding pocket(no: 1) in the query (biounit: 2okl.bio2) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 1NU4 MLA None
2 1UO4 PIH None
3 3KO0 TFP None
4 1UO5 PIH None
5 5AZC PGT None
6 5NNT DPV None
7 2GBB CIT None
8 5M36 9SZ None
9 4GK9 MAN BMA MAN MAN MAN None
10 5Y02 HBX None
11 4RJD TFP None
12 5TVI O8N None
13 5Y02 MXN None
14 4WG0 CHD None
15 5EXA 5SO None
16 2ALG HP6 None
17 2ALG DAO None
18 6BOC RIM None
19 5TVI MYR None
20 1KUK PCA LYS TRP 1.08108
21 3CHT 4NB 1.08108
22 2UXI G50 1.08108
23 1WLJ U5P 1.62162
24 3GZ9 D32 2.16216
25 4BXK 1IU 2.16216
26 5HCN DAO 2.16216
27 3WYJ H78 2.16216
28 1A8P FAD 2.16216
29 2P4Y C03 2.16216
30 3Q2H QHF 2.7027
31 3B9Z CO2 2.7027
32 2YB9 HA0 2.7027
33 6H8S FSZ 2.7027
34 4RW3 TDA 2.7027
35 3U4C NDP 2.7027
36 3G58 988 2.7027
37 1XON PIL 2.7027
38 1XMU ROF 2.7027
39 1XMY ROL 2.7027
40 2OZ5 7XY 2.7027
41 5OHJ 9VE 2.7027
42 1XM4 PIL 2.7027
43 2AMV BIN 2.7027
44 3GWT 066 2.7027
45 1RM8 BAT 2.95858
46 5V4R MGT 3.08642
47 3X1M COA 3.14465
48 6HT0 GQ8 3.22581
49 1ATL 0QI 3.24324
50 4OPC PGT 3.24324
51 4MGA 27L 3.24324
52 4TV1 36M 3.24324
53 1J1R ADE 3.24324
54 6ARJ SAH 3.24324
55 2A1L PCW 3.24324
56 4QHP 32Q 3.24324
57 4MG9 27K 3.24324
58 1VL1 CIT 3.24324
59 1T27 PCW 3.24324
60 4KWD JF2 3.24324
61 4QOM PYG 3.24324
62 1NF8 BOG 3.24324
63 3AI3 SOE 3.24324
64 4K90 MLA 3.24324
65 5N26 CPT 3.2967
66 1JGS SAL 3.62319
67 4NAT ADP 3.75
68 4AIG FLX 3.78378
69 3X01 AMP 3.78378
70 2OUA AES 3.78378
71 3HBV ALA LYS ALA SER GLN ALA ALA 3.78378
72 2V57 PRL 3.78378
73 5KD8 TNR 3.78378
74 5NC1 NAG 3.78378
75 5Z3I ADE 3.78378
76 1XOC VAL ASP SER LYS ASN THR SER SER TRP 3.78378
77 4RFM 3P6 3.78378
78 3VPD CIT 3.78378
79 3C88 ARG ARG GLY CYS NH2 3.78378
80 3H0A D30 3.78378
81 4Q5M ROC 3.78378
82 4C3Y FAD 3.78378
83 3QPB R1P 3.78378
84 3R1V AZB 3.93701
85 2YLD CMO 3.93701
86 3KP6 SAL 3.97351
87 1UUY PPI 4.19162
88 3SE5 ANP 4.26829
89 2J83 BAT 4.32432
90 5O7E 9NB 4.32432
91 5OSW DIU 4.32432
92 6BR8 PGV 4.32432
93 4URX FK1 4.32432
94 2NAD NAD 4.32432
95 1UI0 URA 4.32432
96 4I90 CHT 4.32432
97 5L7G LYS SER LEU LEU GLN GLN LEU LEU THR GLU 4.32432
98 5CX6 CDP 4.32432
99 4OHU NAD 4.32432
100 4OHU 2TK 4.32432
101 2ZWA SAH 4.32432
102 3NFD COA 4.57516
103 1D09 PAL 4.57516
104 5LWY OLB 4.6729
105 5C1M OLC 4.8
106 1Q3A NGH 4.84848
107 1FBL HTA 4.86486
108 1BKC INN 4.86486
109 3O01 DXC 4.86486
110 4DV8 0LX 4.86486
111 2FV5 541 4.86486
112 1ZPD CIT 4.86486
113 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 4.86486
114 4V3I ASP LEU THR ARG PRO 4.86486
115 4AR8 IP8 GLY PRO ALA 4.86486
116 4PGK Y69 4.86486
117 5FQK 6NT 4.86486
118 6B3A SAM 4.86486
119 1K7L 544 4.86486
120 3GKJ HC3 4.86486
121 3SP6 IL2 4.86486
122 2Q8G AZX 4.86486
123 5EK3 5PK 4.86486
124 3AHO 3A2 4.86486
125 5UC9 MYR 4.86726
126 1HFS L04 5
127 5IF4 6AK 5.03145
128 1U4J MAN 5.08475
129 5CHR 4NC 5.10949
130 1MT1 AG2 5.30973
131 1N13 AG2 5.30973
132 2TCL RO4 5.32544
133 2QQD AG2 5.35714
134 2QQC AG2 5.35714
135 2ZXG S23 5.40541
136 5AB0 2X0 7GA LYS HIS HIS ALA PHE SER PHE LYN 5.40541
137 3TDC 0EU 5.40541
138 6BTN E8M 5.40541
139 3CRZ FAD 5.40541
140 3CRZ NAP 5.40541
141 5DUF G7A 5.40541
142 5IUY BOG 5.40541
143 2ZCQ B65 5.40541
144 5G57 6M5 5.40541
145 3V1S 0LH 5.40541
146 1TL2 NDG 5.40541
147 2V5E SCR 5.94059
148 1YP1 LYS ASN LEU 5.94595
149 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 5.94595
150 4WKI 3PW 5.94595
151 4GAA BES 5.94595
152 2Z9I GLY ALA THR VAL 5.94595
153 2XQ0 BES 5.94595
154 5X13 HC4 5.94595
155 1ZED PNP 5.94595
156 2B56 U5P 5.94595
157 3V66 D3A 5.94595
158 6ESN BWE 5.94595
159 4Z1D PEP 5.94595
160 6F6E PLM 5.94595
161 3DST GRG 5.94595
162 5LX9 OLB 5.98592
163 5C9J DAO 6.06061
164 1IDA 0PO 6.06061
165 6GMN F4E 6.18557
166 1R55 097 6.48649
167 2VJ8 HA2 6.48649
168 3W54 RNB 6.48649
169 5IKH 6BW 6.48649
170 4F06 PHB 6.48649
171 2BHW NEX 6.48649
172 5KAU RHQ 6.66667
173 4WZV E40 6.875
174 1T0S BML 6.97674
175 4MA6 28E 7.00637
176 3E70 GDP 7.0122
177 1R6N 434 7.02703
178 4OGQ 2WD 7.02703
179 3OKI OKI 7.02703
180 4OGQ 7PH 7.02703
181 4OGQ 1O2 7.02703
182 3BAZ NAP 7.02703
183 4XU6 TDA 7.02703
184 4DFU QUE 7.45342
185 4WGF HX2 7.56757
186 4YSW NAI 7.56757
187 4YSW FAD 7.56757
188 5V3Y 5V8 7.56757
189 5LOF 70R 7.56757
190 1MMQ RRS 7.64706
191 1MID LAP 7.69231
192 1BWO LPC 7.77778
193 2D5X L35 7.80142
194 5IDM C2E 7.82123
195 1ZVX FIN 7.97546
196 4MRP GSH 8.10811
197 4CA5 3EF 8.10811
198 4KX8 L2O VAL VAL ASP 8.10811
199 3SQP 3J8 8.10811
200 3R9V DXC 8.10811
201 3R6K FUC GAL GLA 8.10811
202 3ROE THM 8.10811
203 1LLU NAD 8.10811
204 5WL1 CUY 8.10811
205 5WL1 D3D 8.10811
206 4M52 M52 8.10811
207 3WV1 WHH 8.18713
208 4IN9 SER TRP PHE PRO 8.43373
209 4R57 ACO 8.52273
210 4DD8 BAT 8.64865
211 3WLE NAD 8.64865
212 5FPN KYD 8.64865
213 3AQT RCO 8.64865
214 6CGN DA 8.64865
215 5KDS A2G THR ALA PRO GLY GLY NAG SIA 8.64865
216 6CWH 6LA 8.79121
217 4UCC ZKW 9.18919
218 4F4S EFO 9.21053
219 5OCA 9QZ 9.52381
220 2BCG GER 9.72973
221 6BMN PAP 9.72973
222 5IM3 DTP 9.72973
223 5W7B MYR 9.72973
224 2VWA PTY 9.90099
225 3ZVS MLI 10
226 4LBP 1WG 10
227 3RV5 DXC 10.1124
228 1HBK COA 10.1124
229 4B6C B5U 10.2703
230 1RTW MP5 10.2703
231 5UGW GSH 10.2857
232 3GXO MQA 10.8108
233 3GF2 SAL 10.9589
234 3HP9 CF1 11.3514
235 3DWB RDF 11.3514
236 3NRZ FAD 11.5854
237 6FX2 FUC C4W NAG BMA MAN NAG GAL 11.6279
238 4Y30 49L 12.4324
239 3QUZ QUV 12.4324
240 2YIV YIV 12.973
241 1SBR VIB 12.973
242 4YHQ G10 13.1313
243 2W14 WR2 13.5135
244 4ZW3 4S9 13.5135
245 2QZT PLM 13.5135
246 3N7S 3N7 13.5417
247 2YFB SIN 13.5659
248 5KVM THR TYR PHE ALA VAL LEU MET VAL SER 14.0541
249 3T3C 017 14.1414
250 2P3C 3TL 14.1414
251 1Y4Z PCI 14.5946
252 4OB6 S2T 15.1351
253 5T2Z 017 15.1515
254 1RV1 IMZ 15.2941
255 3WCA FPS 15.6757
256 5CSD ACD 16.3522
257 2GWH PCI 16.7568
258 3KIF GDL 16.9811
259 5C9P FUC 17.8378
260 1R5L VIV 18.3784
261 5Z84 CHD 21.4286
262 5ZCO CHD 21.4286
263 5W97 CHD 21.4286
264 2DYS PGV 21.4286
265 3W68 VIV 25.4054
266 1COY FAD 27.027
267 2Y69 CHD 36.5079
268 5MTE BB2 40.8759
269 1G27 BB1 42.2619
270 1RL4 BRR 47.027
Pocket No.: 2; Query (leader) PDB : 2OKL; Ligand: BB2; Similar sites found with APoc: 35
This union binding pocket(no: 2) in the query (biounit: 2okl.bio2) has 6 residues
No: Leader PDB Ligand Sequence Similarity
1 3D3W NAP None
2 1PR9 NAP None
3 1XHL NDP 1.62162
4 3AY6 NAI 1.62162
5 2DKN NAI 2.16216
6 4J7U YTZ 2.7027
7 4J7U NAP 2.7027
8 2PS1 PRP 2.7027
9 5BJX NAD 3.24324
10 4O0L NDP 3.24324
11 5OMY 9YE 3.78378
12 3EWA ANP 4.32432
13 3G5N PB2 4.86486
14 2FR1 NDP 5.40541
15 1XKQ NDP 5.40541
16 3FYH ADP 5.40541
17 4G5H UD7 5.50964
18 4G5H NAP 5.50964
19 1J09 ATP 5.94595
20 1J09 GLU 5.94595
21 2FSH ANP 5.94595
22 4HXY NDP 5.94595
23 4CQM NAP 5.94595
24 4TR9 ASP TRP ASN 7.02703
25 2JAP NDP 7.02703
26 2H21 SAM 7.02703
27 6BWL NAD 7.56757
28 3VZS NAP 7.56757
29 3VZS CAA 7.56757
30 5KJK SAM 8.10811
31 5KJK 6T1 8.10811
32 3HNC TTP 9.72973
33 4GLL NAD 13.5135
34 5H3A D16 14.0541
35 3B7G ANP 14.5946
Pocket No.: 3; Query (leader) PDB : 2OKL; Ligand: BB2; Similar sites found with APoc: 33
This union binding pocket(no: 3) in the query (biounit: 2okl.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 1XZ3 ICF None
2 1M2Z BOG 1.62162
3 5O2N FLC 2.7027
4 4DS0 A2G GAL NAG FUC 3.06748
5 1LNX URI 3.7037
6 2HW1 FRU 3.78378
7 2GSD NAD 4.32432
8 2C78 PUL 4.32432
9 6BVI EC4 4.32432
10 6BVJ EAS 4.32432
11 1A5Z FBP 4.32432
12 4LEB THR THR THR THR THR THR THR 4.32432
13 1VAY AZA 4.32432
14 6BVL EBY 4.32432
15 3ENV ABF 4.86486
16 5FUS DAO 4.86486
17 3O5N BR0 5.35714
18 5TCI 79V 5.43478
19 1GJW GLC 5.94595
20 4L8F MTX 7.02703
21 3COW 52H 7.02703
22 2O4N TPV 7.07071
23 1FIQ FAD 8.6758
24 4Q9M FPP 9.18919
25 2D5Z L35 9.21986
26 1LYX PGA 9.72973
27 4E5N NAD 10.8108
28 4GDX GLU 10.8108
29 3RLF MAL 12.973
30 4G31 0WH 15.1351
31 5TWB FAD 16.7568
32 5Z84 PGV 21.4286
33 2DYR PGV 21.4286
Pocket No.: 4; Query (leader) PDB : 2OKL; Ligand: BB2; Similar sites found with APoc: 5
This union binding pocket(no: 4) in the query (biounit: 2okl.bio1) has 5 residues
No: Leader PDB Ligand Sequence Similarity
1 1EYN 2AN 3.24324
2 3BK2 U5P 3.24324
3 4ZY1 4U5 8.64865
4 1FDJ 13P 13.5135
5 1FDJ 2FP 13.5135
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