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Receptor
PDB id Resolution Class Description Source Keywords
3G5K 1.7 Å EC: 3.5.1.88 STRUCTURE AND ACTIVITY OF HUMAN MITOCHONDRIAL PEPTIDE DEFORM NOVEL CANCER TARGET HOMO SAPIENS PEPTIDE DEFORMYLASE ACTINONIN HYDROLASE IRON METAL-BINDIMITOCHONDRION PROTEIN BIOSYNTHESIS TRANSIT PEPTIDE
Ref.: STRUCTURE AND ACTIVITY OF HUMAN MITOCHONDRIAL PEPTI DEFORMYLASE, A NOVEL CANCER TARGET J.MOL.BIOL. V. 387 1211 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BB2 A:1001;
B:1002;
C:1003;
D:1004;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
385.498 C19 H35 N3 O5 CCCCC...
CO A:1002;
B:1003;
C:1;
D:2;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
58.933 Co [Co+2...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3G5K 1.7 Å EC: 3.5.1.88 STRUCTURE AND ACTIVITY OF HUMAN MITOCHONDRIAL PEPTIDE DEFORM NOVEL CANCER TARGET HOMO SAPIENS PEPTIDE DEFORMYLASE ACTINONIN HYDROLASE IRON METAL-BINDIMITOCHONDRION PROTEIN BIOSYNTHESIS TRANSIT PEPTIDE
Ref.: STRUCTURE AND ACTIVITY OF HUMAN MITOCHONDRIAL PEPTI DEFORMYLASE, A NOVEL CANCER TARGET J.MOL.BIOL. V. 387 1211 2009
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 3G5K - BB2 C19 H35 N3 O5 CCCCC[C@H]....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 3G5K - BB2 C19 H35 N3 O5 CCCCC[C@H]....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3G5K - BB2 C19 H35 N3 O5 CCCCC[C@H]....
2 4JE8 Kd = 6100 nM MET ALA SER n/a n/a
3 4JE7 Kd = 395 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
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 : 3G5K; Ligand: BB2; Similar sites found with APoc: 278
This union binding pocket(no: 1) in the query (biounit: 3g5k.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 1KUK PCA LYS TRP None
2 1UO4 PIH None
3 5NNT DPV None
4 3KP6 SAL None
5 2VWA PTY None
6 3R1V AZB None
7 1UO5 PIH None
8 5CHR 4NC None
9 4UA3 COA None
10 4PYA 2X3 None
11 2J9L ATP None
12 4B52 RDF None
13 2UXI G50 None
14 4WG0 CHD None
15 5CSD ACD None
16 5C2N NAG None
17 5N5U 7N8 None
18 2FKW RG1 None
19 5Z3I ADE 1.0929
20 3WV1 WHH 1.16959
21 1ATL 0QI 1.63934
22 3KC1 2T6 1.63934
23 5TWB FAD 1.63934
24 3NK7 SAM 1.63934
25 5A0R ACE GLU VAL ASN PRO 1.63934
26 1MMQ RRS 1.76471
27 5V4R MGT 1.85185
28 3Q2H QHF 2.18579
29 1OUK 084 2.18579
30 4PGK Y69 2.18579
31 3CHT 4NB 2.18579
32 3G9E RO7 2.18579
33 5EK3 5PK 2.18579
34 2A9D MTE 2.18579
35 3FUR Z12 2.18579
36 3ET3 ET1 2.18579
37 5ZI7 GLU 2.18579
38 1TL2 NDG 2.18579
39 2YFB SIN 2.32558
40 1ZVX FIN 2.45399
41 4RW3 TDA 2.73224
42 1R6N 434 2.73224
43 4FAJ LEU VAL THR LEU VAL PHE VAL 2.73224
44 5KD8 TNR 2.73224
45 3COW 52H 2.73224
46 5OSW DIU 2.73224
47 2XQ0 BES 2.73224
48 4WGF HX2 2.73224
49 3X01 AMP 2.73224
50 5J6A P46 2.73224
51 3AQT RCO 2.73224
52 3LKF PC 2.73224
53 4K90 MLA 2.73224
54 4REP FAD 2.73224
55 4XU6 TDA 2.73224
56 2ZCQ B65 2.73224
57 3V1S 0LH 2.73224
58 1F7K UMP 2.94118
59 4WZV E40 3.125
60 4WKI 3PW 3.27869
61 4DD8 BAT 3.27869
62 2ZXG S23 3.27869
63 2VJ8 HA2 3.27869
64 4GAA BES 3.27869
65 4RFM 3P6 3.27869
66 1RJD SAM 3.27869
67 4V3I ASP LEU THR ARG PRO 3.27869
68 5DUF G7A 3.27869
69 5IUY BOG 3.27869
70 1VAY AZA 3.27869
71 5NJI 8Z2 3.27869
72 1J1R ADE 3.27869
73 2BCG GER 3.27869
74 2OBD PCW 3.27869
75 5HCN DAO 3.27869
76 4N14 WR7 3.27869
77 6ARJ SAH 3.27869
78 5G57 6M5 3.27869
79 1YKD CMP 3.27869
80 4MRP GSH 3.27869
81 5N26 CPT 3.2967
82 1BWO LPC 3.33333
83 4R57 ACO 3.40909
84 1RM8 BAT 3.5503
85 5KAU RHQ 3.63636
86 4ZW3 4S9 3.82514
87 1YP1 LYS ASN LEU 3.82514
88 4AR8 IP8 GLY PRO ALA 3.82514
89 5LX9 OLB 3.82514
90 1C3X 8IG 3.82514
91 3C88 ARG ARG GLY CYS NH2 3.82514
92 1GEG GLC 3.82514
93 4IGH 1EA 3.82514
94 4IGH ORO 3.82514
95 4IGH FMN 3.82514
96 1ZED PNP 3.82514
97 4RHP PEF 3.82514
98 2Q8G AZX 3.82514
99 3DWB RDF 3.82514
100 4F06 PHB 3.82514
101 1DL5 SAH 3.82514
102 1COY FAD 3.82514
103 3KXC PLM 3.82514
104 1WLJ U5P 3.82514
105 1ZPD CIT 3.82514
106 3O01 DXC 4.37158
107 2W14 WR2 4.37158
108 5O7E 9NB 4.37158
109 5AB0 2X0 7GA LYS HIS HIS ALA PHE SER PHE LYN 4.37158
110 4QHP 32Q 4.37158
111 5FPN KYD 4.37158
112 3G4G D71 4.37158
113 1XON PIL 4.37158
114 6BR8 PGV 4.37158
115 3G58 988 4.37158
116 6C5B SAH 4.37158
117 5AZC PGT 4.37158
118 3R9V DXC 4.37158
119 3AHO 3A2 4.37158
120 3E1T FAD 4.37158
121 2RCU BUJ 4.37158
122 2A1L PCW 4.37158
123 3EE4 MYR 4.37158
124 5EHR 5OD 4.37158
125 2IHU TP9 4.37158
126 4RJD TFP 4.54545
127 1UUY PPI 4.79042
128 5FVJ ACO 4.81928
129 1Q3A NGH 4.84848
130 2GWH PCI 4.91803
131 1R55 097 4.91803
132 2YB9 HA0 4.91803
133 4NMC FAD 4.91803
134 4NMC 2OP 4.91803
135 3PE2 E1B 4.91803
136 1SOX MTE 4.91803
137 6H8S FSZ 4.91803
138 5X8G S0N 4.91803
139 3SFI 3SF 4.91803
140 3ZVS MLI 5
141 4NAT ADP 5
142 3SQP 3J8 5.02092
143 1USF NAP 5.05618
144 5B0W 22B 5.15464
145 1VLH PNS 5.20231
146 3B9Z CO2 5.46448
147 3GKJ HC3 5.46448
148 3TDC 0EU 5.46448
149 3H0A D30 5.46448
150 3HBV ALA LYS ALA SER GLN ALA ALA 5.46448
151 5OHJ 9VE 5.46448
152 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 5.46448
153 3GWT 066 5.46448
154 2V57 PRL 5.46448
155 1XM4 PIL 5.46448
156 1XMU ROF 5.46448
157 1R5L VIV 5.46448
158 1XMY ROL 5.46448
159 4TMN 0PK 5.46448
160 4UCC ZKW 5.46448
161 2D5Z L35 5.47945
162 3X1M COA 5.66038
163 3WR7 COA 5.88235
164 4KX8 L2O VAL VAL ASP 6.01093
165 5O2N FLC 6.01093
166 2YIV YIV 6.01093
167 3QDK QDK 6.01093
168 3W68 VIV 6.01093
169 1N8V BDD 6.25
170 3QLM PLM 6.45161
171 2FV5 541 6.55738
172 1BKC INN 6.55738
173 3H0L ADP 6.55738
174 4B6C B5U 6.55738
175 5KVM THR TYR PHE ALA VAL LEU MET VAL SER 6.55738
176 3WCA FPS 6.55738
177 3QFA FAD 6.55738
178 4IN9 SER TRP PHE PRO 6.62651
179 5UGW GSH 6.85714
180 2TCL RO4 7.10059
181 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 7.10383
182 1FBL HTA 7.10383
183 2B56 U5P 7.10383
184 1J78 OLA 7.10383
185 5TO8 7FM 7.10383
186 4YMX ARG 7.10383
187 2XVD AS6 7.10383
188 3NFD COA 7.18954
189 1HFS L04 7.5
190 2ZWA SAH 7.65027
191 3DJF BC3 7.65027
192 4QOM PYG 7.65027
193 1FIQ FAD 7.65027
194 1MT1 AG2 7.9646
195 1T0S BML 8.13953
196 4DV8 0LX 8.19672
197 5CX6 CDP 8.19672
198 4H6Q TFB 8.19672
199 3KDU NKS 8.19672
200 4C2C ALA ALA ALA 8.19672
201 4I90 CHT 8.19672
202 5IM3 DTP 8.19672
203 5DK4 5BX 8.19672
204 5DK4 ATP 8.19672
205 3N7S 3N7 8.69565
206 2ALG DAO 8.69565
207 2ALG HP6 8.69565
208 3NB0 G6P 8.74317
209 5Z84 CHD 8.84354
210 5ZCO CHD 8.84354
211 5W97 CHD 8.84354
212 3KO0 TFP 8.91089
213 2GBB CIT 8.97436
214 4P6X HCY 9.28962
215 3RUG DB6 9.28962
216 5V3Y 5V8 9.28962
217 5K52 OCD 9.28962
218 6CS8 F9Y 9.28962
219 1SQL GUN 9.58904
220 5TVI O8N 9.78261
221 5LWY OLB 9.83607
222 4GK9 MAN BMA MAN MAN MAN 9.83607
223 5KF6 FAD 9.83607
224 5KF6 TFB 9.83607
225 2Z9I GLY ALA THR VAL 9.83607
226 2YPO PHE 9.83607
227 2QZT PLM 9.90991
228 4ZVI 4S4 10.3825
229 4F4S EFO 10.5263
230 2J83 BAT 10.929
231 5C9P FUC 10.929
232 4D4U FUC 10.929
233 4J56 FAD 10.929
234 2BIF BOG 10.929
235 5TCI 79V 11.2319
236 2FP2 TSA 11.4458
237 4OGQ 2WD 11.4754
238 1VA6 ADP 11.4754
239 1VA6 P2S 11.4754
240 5IFK HPA 11.4754
241 4OGQ 7PH 11.4754
242 1VMK GUN 11.4754
243 5OCA 9QZ 11.7647
244 4CA5 3EF 12.0219
245 3W54 RNB 12.0219
246 6BMN PAP 12.0219
247 4ZGM 32M 12.2951
248 4MN3 ACE PHE ALA TYR M3L SER NH2 12.5
249 1TIW TFB 12.5683
250 1TIW FAD 12.5683
251 4TV1 36M 12.5683
252 5AAV GW5 12.5683
253 2QE4 JJ3 12.5683
254 1M2Z BOG 13.1148
255 5M36 9SZ 13.1579
256 4LY9 1YY 13.6612
257 4LY9 S6P 13.6612
258 6DQU GLY ILE ILE ASN THR LEU 13.6612
259 2Y69 CHD 14.2012
260 2AX9 BHM 14.2077
261 1XVB BHL 14.7541
262 2V5E SCR 14.8515
263 1NU4 MLA 15.4639
264 3GZ9 D32 15.847
265 3E5A VX6 15.9091
266 4WO4 JLS 16
267 5C9J DAO 16.1616
268 3HUJ AGH 16.1616
269 6F6E PLM 16.3934
270 4AIG FLX 16.9399
271 6BTN E8M 17.4863
272 3ZJ0 ACO 19.1257
273 4BXK 1IU 21.3115
274 5A4W QCT 31.1475
275 1RL4 BRR 43.1694
276 5MTE BB2 44.5255
277 1G27 BB1 47.619
278 3UWB BB2 49.3507
Pocket No.: 2; Query (leader) PDB : 3G5K; Ligand: BB2; Similar sites found with APoc: 31
This union binding pocket(no: 2) in the query (biounit: 3g5k.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 5UC9 MYR None
2 3OCP CMP None
3 2ZL4 ALA ALA ALA ALA None
4 4YV5 SVR 2.45902
5 6CB2 OLC 2.73224
6 4RC8 STE 2.73224
7 4G86 BNT 3.27869
8 1EWF PC1 3.27869
9 2Z3U CRR 3.82514
10 3ENV ABF 3.82514
11 5K53 STE 3.82514
12 4R5M 4NO 4.37158
13 5NM7 GLY 4.37158
14 3ND6 ATP 4.67836
15 3E70 GDP 4.91803
16 2V3V MGD 5.46448
17 2BHW NEX 5.46448
18 2YVF FAD 5.46448
19 1IXI 2HP 5.46448
20 1UY4 XYP XYP XYP XYP 6.89655
21 4LO6 SIA GAL 7.65027
22 5ZCO PEK 8.84354
23 3ZUY TCH 10.3825
24 1N13 AG2 10.6195
25 2QQC AG2 10.7143
26 2QQD AG2 10.7143
27 1B7H LYS NLE LYS 13.6612
28 3KV8 FAH 14.3885
29 3RMK BML 14.7541
30 5L7G LYS SER LEU LEU GLN GLN LEU LEU THR GLU 15.3005
31 3HP9 CF1 16.9399
Pocket No.: 3; Query (leader) PDB : 3G5K; Ligand: BB2; Similar sites found with APoc: 21
This union binding pocket(no: 3) in the query (biounit: 3g5k.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 4F8L AES 2.06897
2 3WYJ H78 2.73224
3 3AB1 FAD 2.73224
4 5HGZ ACO 3.82514
5 4UMJ BFQ 3.82514
6 5KAX RHQ 4.81928
7 4COL DTP 4.91803
8 3WDM ADN 4.91803
9 2ED4 FAD 5.36913
10 5O0B 9FE 6.79012
11 3U3U EAH 7.10383
12 1K7L 544 8.19672
13 2I0G I0G 8.19672
14 4IJ6 SEP 8.19672
15 1TT8 PHB 9.7561
16 4BNU 9KQ 12.5683
17 4MGA 27L 12.5683
18 1U2Z SAH 18.5792
19 2E2R 2OH 19.1257
20 3L9R L9R 20.4082
21 3OKI OKI 35.7143
Pocket No.: 4; Query (leader) PDB : 3G5K; Ligand: BB2; Similar sites found with APoc: 16
This union binding pocket(no: 4) in the query (biounit: 3g5k.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 5N1X 8HH None
2 4OIV XX9 None
3 2IV2 MGD 1.0929
4 2P4Y C03 2.18579
5 4CZG QH3 3.27869
6 5MZI FYK 3.27869
7 2ZFU SAH 4.37158
8 5B4B LP5 4.91803
9 4NWJ 3PG 6.01093
10 4UBS DIF 6.01093
11 4EUU BX7 6.01093
12 5C1M OLC 6.4
13 5JKG 6LF 7.10383
14 4WZ8 3W7 8.19672
15 1SBR VIB 12.5683
16 5EEH P9P 13.1148
Pocket No.: 5; Query (leader) PDB : 3G5K; Ligand: BB2; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 3g5k.bio3) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 3G5K; Ligand: BB2; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 3g5k.bio3) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 3G5K; Ligand: BB2; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 3g5k.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 3G5K; Ligand: BB2; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 3g5k.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
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