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...
View in 3D viewer
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 4 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: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3g5k.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3G5K; Ligand: BB2; Similar sites found: 107
This union binding pocket(no: 2) in the query (biounit: 3g5k.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4GQL R47 0.0004976 0.48524 None
2 1KUK PCA LYS TRP 0.00009811 0.46823 None
3 2VWA PTY 0.005351 0.43691 None
4 1UO5 PIH 0.01891 0.42046 None
5 3R1V AZB 0.007923 0.4133 None
6 5UC9 MYR 0.01129 0.40972 None
7 5CSD ACD 0.02628 0.40403 None
8 3KP6 SAL 0.01858 0.4035 None
9 2ZL4 ALA ALA ALA ALA 0.02219 0.40106 None
10 4UA3 COA 0.0108 0.40056 None
11 3WV1 WHH 0.001369 0.46969 1.16959
12 1ATL 0QI 0.00006192 0.50631 1.63934
13 1MMQ RRS 0.0001461 0.46802 1.76471
14 5V4R MGT 0.0002995 0.50313 1.85185
15 3Q2H QHF 0.00002319 0.49215 2.18579
16 3ET3 ET1 0.01088 0.4004 2.18579
17 1ZVX FIN 0.0002602 0.49611 2.45399
18 4RW3 TDA 0.0008848 0.47767 2.73224
19 4PJT 2YQ 0.009333 0.41818 2.73224
20 3LKF PC 0.02729 0.4131 2.73224
21 4RC8 STE 0.01164 0.40245 2.73224
22 4K90 MLA 0.02545 0.40105 2.73224
23 4WZV E40 0.0006247 0.46421 3.125
24 4WKI 3PW 0.000006855 0.55084 3.27869
25 2ZXG S23 0.0002435 0.4849 3.27869
26 4DD8 BAT 0.000006757 0.48341 3.27869
27 4GAA BES 0.0009809 0.44106 3.27869
28 1RJD SAM 0.008416 0.40723 3.27869
29 5NJI 8Z2 0.01719 0.40051 3.27869
30 1BWO LPC 0.005347 0.41249 3.33333
31 1RM8 BAT 0.00006582 0.45218 3.5503
32 1YP1 LYS ASN LEU 0.000003947 0.4937 3.82514
33 4ZW3 4S9 0.0003344 0.4909 3.82514
34 4AR8 IP8 GLY PRO ALA 0.00057 0.4515 3.82514
35 1GEG GLC 0.01702 0.43044 3.82514
36 3C88 ARG ARG GLY CYS NH2 0.02603 0.4103 3.82514
37 2Z7I 742 0.04983 0.40772 3.82514
38 4IGH FMN 0.04975 0.40664 3.82514
39 4IGH ORO 0.04975 0.40664 3.82514
40 4IGH 1EA 0.04975 0.40664 3.82514
41 4RHP PEF 0.00673 0.40397 3.82514
42 5K53 STE 0.0107 0.40074 3.82514
43 2W14 WR2 0.0001423 0.47016 4.37158
44 4ARF IP8 GLY PRO ALA 0.0002702 0.46585 4.37158
45 3R9V DXC 0.001516 0.46162 4.37158
46 4QHP 32Q 0.001723 0.43855 4.37158
47 3G4G D71 0.004366 0.41644 4.37158
48 1XON PIL 0.01047 0.41196 4.37158
49 3G58 988 0.002271 0.40707 4.37158
50 5FVJ ACO 0.01018 0.41116 4.81928
51 1Q3A NGH 0.00001279 0.48989 4.84848
52 3HY9 098 0.000006262 0.54401 4.91803
53 1R55 097 0.0000213 0.47804 4.91803
54 2YB9 HA0 0.02147 0.42561 4.91803
55 4NMC 2OP 0.02193 0.40592 4.91803
56 4NMC FAD 0.02298 0.40592 4.91803
57 3PE2 E1B 0.03831 0.40029 4.91803
58 3ZVS MLI 0.0002954 0.43161 5
59 4NAT ADP 0.038 0.42005 5
60 3B9Z CO2 0.002374 0.46198 5.46448
61 3TDC 0EU 0.01424 0.43242 5.46448
62 2V3V MGD 0.03302 0.4198 5.46448
63 1XM4 PIL 0.004777 0.4188 5.46448
64 3GKJ HC3 0.004837 0.41635 5.46448
65 3H0A D30 0.009515 0.41253 5.46448
66 3HBV ALA LYS ALA SER GLN ALA ALA 0.002682 0.41108 5.46448
67 2YVF FAD 0.04899 0.40525 5.46448
68 1R5L VIV 0.01286 0.40355 5.46448
69 1XMU ROF 0.008997 0.40207 5.46448
70 4UCC ZKW 0.02574 0.40052 5.46448
71 2D5Z L35 0.02006 0.43273 5.47945
72 4KX8 L2O VAL VAL ASP 0.001426 0.44033 6.01093
73 3W68 VIV 0.01105 0.40184 6.01093
74 1BKC INN 0.00002286 0.49474 6.55738
75 2FV5 541 0.000006476 0.42962 6.55738
76 5KVM THR TYR PHE ALA VAL LEU MET VAL SER 0.01542 0.40781 6.55738
77 4B6C B5U 0.007558 0.40173 6.55738
78 1UY4 XYP XYP XYP XYP 0.01477 0.40927 6.89655
79 2TCL RO4 0.0001249 0.48804 7.10059
80 1FBL HTA 0.00003167 0.48284 7.10383
81 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 0.008761 0.43729 7.10383
82 1J78 OLA 0.009159 0.40011 7.10383
83 3NFD COA 0.01514 0.40346 7.18954
84 1HFS L04 0.0006936 0.47305 7.5
85 2ZWA SAH 0.006362 0.41448 7.65027
86 3DJF BC3 0.01343 0.40117 7.65027
87 1T0S BML 0.003864 0.43062 8.13953
88 4DV8 0LX 0.0002539 0.49662 8.19672
89 3KDU NKS 0.01857 0.41043 8.19672
90 3KO0 TFP 0.005094 0.44167 8.91089
91 4P6X HCY 0.008984 0.42018 9.28962
92 5K52 OCD 0.01137 0.40126 9.28962
93 2Z9I GLY ALA THR VAL 0.005603 0.43865 9.83607
94 5KF6 TFB 0.01939 0.40534 9.83607
95 5KF6 FAD 0.01939 0.40534 9.83607
96 2QZT PLM 0.003744 0.43289 9.90991
97 2J83 BAT 0.00002319 0.52104 10.929
98 1TIW TFB 0.03099 0.40051 12.5683
99 1TIW FAD 0.03099 0.40051 12.5683
100 1B7H LYS NLE LYS 0.02311 0.40167 13.6612
101 2Y69 CHD 0.009885 0.41938 14.2012
102 3KV8 FAH 0.03875 0.4093 14.3885
103 2V5E SCR 0.006238 0.42819 14.8515
104 4AIG FLX 0.00005356 0.4703 16.9399
105 1RL4 BRR 0.0000000007567 0.77443 43.1694
106 1G27 BB1 0.00000000002061 0.73483 47.619
107 3UWB BB2 0.000000001208 0.61611 49.3507
Pocket No.: 3; Query (leader) PDB : 3G5K; Ligand: BB2; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3g5k.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3G5K; Ligand: BB2; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 3g5k.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 3G5K; Ligand: BB2; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 3G5K; Ligand: BB2; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 3G5K; Ligand: BB2; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 3G5K; Ligand: BB2; Similar sites found: 35
This union binding pocket(no: 8) in the query (biounit: 3g5k.bio2) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5EPK 5R0 PHE ALA LEU ELY 5R5 0.003736 0.41096 None
2 4OIV XX9 0.027 0.40665 None
3 2IV2 MGD 0.01461 0.41796 1.0929
4 2XXP DSL 0.04724 0.41243 1.0929
5 3KC1 2T6 0.007446 0.40981 1.63934
6 3DBK RDF 0.00874 0.4066 1.63934
7 3NK7 SAM 0.009591 0.40657 1.63934
8 3G9E RO7 0.01143 0.41995 2.18579
9 3FUR Z12 0.03548 0.40584 2.18579
10 2XQ0 BES 0.002312 0.40676 2.73224
11 1F7K UMP 0.006628 0.40811 2.94118
12 4CZG QH3 0.02188 0.40824 3.27869
13 3DWB RDF 0.00646 0.40071 3.82514
14 2A1L PCW 0.03681 0.40339 4.37158
15 3E1T FAD 0.04246 0.40104 4.37158
16 2ZFU SAH 0.01443 0.40003 4.37158
17 5KAX RHQ 0.01852 0.40142 4.81928
18 5B4B LP5 0.01883 0.40462 4.91803
19 3GWT 066 0.01301 0.41486 5.46448
20 3WCA FPS 0.01697 0.4068 6.55738
21 5JKG 6LF 0.02912 0.40308 7.10383
22 4QOM PYG 0.01262 0.40104 7.65027
23 4H6Q TFB 0.008301 0.42178 8.19672
24 2ALG HP6 0.01207 0.40365 8.69565
25 2ALG DAO 0.01207 0.40365 8.69565
26 4ZVI 4S4 0.009927 0.40405 10.3825
27 4CA5 3EF 0.004426 0.45516 12.0219
28 4MN3 ACE PHE ALA TYR M3L SER NH2 0.006979 0.40492 12.5
29 4BNU 9KQ 0.01148 0.40633 12.5683
30 4LY9 S6P 0.04554 0.40181 13.6612
31 4LY9 1YY 0.04861 0.40181 13.6612
32 1XVB BHL 0.02993 0.4044 14.7541
33 3HUJ AGH 0.04743 0.40014 16.1616
34 3L9R L9R 0.02652 0.402 20.4082
35 4BXK 1IU 0.003238 0.45025 21.3115
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