Receptor
PDB id Resolution Class Description Source Keywords
1LQY 1.9 Å EC: 3.5.1.88 CRYSTAL STRUCTURE OF BACILLUS STEAROTHERMOPHILUS PEPTIDE DEFORMYLASE COMPLEXED WITH ANTIBIOTIC ACTINONIN GEOBACILLUS STEAROTHERMOPHILUS ACTINONIN INHIBITION POLYPEPTIDE DEFORMYLASE HYDROLASE
Ref.: THE CRYSTAL STRUCTURES OF FOUR PEPTIDE DEFORMYLASES BOUND TO THE ANTIBIOTIC ACTINONIN REVEAL TWO DISTINCT TYPES: A PLATFORM FOR THE STRUCTURE-BASED DESIGN OF ANTIBACTERIAL AGENTS. J.MOL.BIOL. V. 320 951 2002
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BB2 A:401;
Valid;
none;
submit data
385.498 C19 H35 N3 O5 CCCCC...
NI A:301;
A:302;
Part of Protein;
Part of Protein;
none;
none;
submit data
58.693 Ni [Ni+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1LQY 1.9 Å EC: 3.5.1.88 CRYSTAL STRUCTURE OF BACILLUS STEAROTHERMOPHILUS PEPTIDE DEFORMYLASE COMPLEXED WITH ANTIBIOTIC ACTINONIN GEOBACILLUS STEAROTHERMOPHILUS ACTINONIN INHIBITION POLYPEPTIDE DEFORMYLASE HYDROLASE
Ref.: THE CRYSTAL STRUCTURES OF FOUR PEPTIDE DEFORMYLASES BOUND TO THE ANTIBIOTIC ACTINONIN REVEAL TWO DISTINCT TYPES: A PLATFORM FOR THE STRUCTURE-BASED DESIGN OF ANTIBACTERIAL AGENTS. J.MOL.BIOL. V. 320 951 2002
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 1LQY - 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 4 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 : 1LQY; Ligand: BB2; Similar sites found: 102
This union binding pocket(no: 1) in the query (biounit: 1lqy.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4DD8 BAT 0.00001803 0.45763 None
2 4NAT ADP 0.03997 0.41601 None
3 5UC9 MYR 0.01231 0.40987 None
4 4RC8 STE 0.001025 0.44626 1.63043
5 1KUK PCA LYS TRP 0.00003073 0.47939 2.17391
6 5K52 OCD 0.00151 0.43687 2.17391
7 3EE4 MYR 0.00205 0.43096 2.17391
8 1K7L 544 0.003447 0.42765 2.17391
9 3FEI CTM 0.007576 0.40905 2.17391
10 1MMQ RRS 0.00004703 0.49639 2.35294
11 2W14 WR2 0.00001597 0.4983 2.71739
12 4AR8 IP8 GLY PRO ALA 0.0002262 0.47177 2.71739
13 4AIG FLX 0.00003638 0.46737 2.71739
14 3GKJ HC3 0.003969 0.41637 2.71739
15 3WCA FPS 0.008082 0.41502 2.71739
16 3KFC 61X 0.01389 0.40783 2.71739
17 5Y3N 8MF 0.01153 0.40698 2.71739
18 4ZBR NPS 0.01376 0.40683 2.71739
19 4ZBR DIF 0.01459 0.40683 2.71739
20 2ZCQ B65 0.02404 0.40644 2.71739
21 3WV1 WHH 0.0003671 0.49272 2.92398
22 2TCL RO4 0.00006822 0.49428 2.95858
23 1RM8 BAT 0.0002728 0.42518 2.95858
24 5V4R MGT 0.0001238 0.51827 3.08642
25 4WZV E40 0.0001012 0.49518 3.125
26 4GAA BES 0.0001889 0.46235 3.26087
27 4UCC ZKW 0.01035 0.43002 3.26087
28 2XQ0 BES 0.0006435 0.4112 3.26087
29 3EWC MCF 0.007893 0.4098 3.26087
30 3QVP FAD 0.02284 0.40838 3.26087
31 4QOM PYG 0.008058 0.40276 3.26087
32 4XMF HSM 0.02784 0.40212 3.26087
33 2C7G FAD 0.04569 0.40153 3.26087
34 1KAP GLY SER ASN SER 0.00287 0.4002 3.26087
35 1ATL 0QI 0.000009161 0.53769 3.80435
36 1R55 097 0.0000172 0.4678 3.80435
37 3HBV ALA LYS ALA SER GLN ALA ALA 0.0003804 0.43733 3.80435
38 4RW3 TDA 0.005985 0.43351 3.80435
39 4ARF IP8 GLY PRO ALA 0.001244 0.4282 3.80435
40 2V3V MGD 0.02852 0.42012 3.80435
41 5HCN DAO 0.01095 0.41699 3.80435
42 3ET3 ET1 0.008227 0.40236 3.80435
43 4BXK 1IU 0.001053 0.46513 4.34783
44 3AHO 3A2 0.003992 0.42319 4.34783
45 4IGH FMN 0.04551 0.40586 4.34783
46 4IGH 1EA 0.04551 0.40586 4.34783
47 4IGH ORO 0.04551 0.40586 4.34783
48 3OKI OKI 0.02766 0.40083 4.34783
49 3FAL LO2 0.01855 0.40079 4.34783
50 1BWO LPC 0.005389 0.4086 4.44444
51 3R1V AZB 0.005669 0.4163 4.72441
52 1FBL HTA 0.00005543 0.46226 4.8913
53 4KX8 L2O VAL VAL ASP 0.0004756 0.45706 4.8913
54 2YOO K2B 0.008392 0.40013 4.8913
55 2QZT PLM 0.005432 0.42159 5.40541
56 3ZJX BOG 0.02315 0.40145 5.43478
57 3HY9 098 0.00001408 0.52193 5.97826
58 3DBK RDF 0.001892 0.42857 5.97826
59 2OBD PCW 0.01225 0.40796 5.97826
60 2ZWA SAH 0.008709 0.4047 5.97826
61 1Q3A NGH 0.00002582 0.46779 6.06061
62 1YP1 LYS ASN LEU 0.000004805 0.4775 6.52174
63 3WYJ H78 0.03216 0.41297 6.52174
64 3KXC PLM 0.00786 0.40988 6.52174
65 3PF7 MLA 0.0167 0.4063 6.52174
66 5IR4 ZPE 0.02337 0.40617 6.52174
67 4B6C B5U 0.006988 0.40363 6.52174
68 1ZVX FIN 0.0001563 0.50142 6.74847
69 2VJ8 HA2 0.0006044 0.4801 7.06522
70 3Q2H QHF 0.000004639 0.54307 7.6087
71 4QHP 32Q 0.001695 0.43463 7.6087
72 1HN4 MJI 0.01309 0.43333 7.63359
73 4CA5 3EF 0.0009723 0.47942 8.15217
74 2J83 BAT 0.0001069 0.48568 8.69565
75 1B7H LYS NLE LYS 0.0162 0.40584 8.69565
76 4ZW3 4S9 0.0001455 0.50288 9.23913
77 2IV2 MGD 0.006756 0.42704 9.23913
78 4DV8 0LX 0.00007663 0.51591 9.78261
79 3G9E RO7 0.007934 0.42037 9.78261
80 4YMX ARG 0.01373 0.40333 9.78261
81 2ZXG S23 0.0003327 0.47368 10.3261
82 2ZB3 NDP 0.01506 0.40254 10.3261
83 3V66 D3A 0.01787 0.40996 10.8696
84 4B52 RDF 0.002508 0.40898 10.8696
85 4ZOM 4Q3 0.04713 0.40834 10.8696
86 3SQP 3J8 0.006158 0.43608 11.413
87 4WKI 3PW 0.00001343 0.49254 11.9565
88 2ALG DAO 0.01003 0.40028 11.9565
89 2ALG HP6 0.01003 0.40028 11.9565
90 5FQK 6NT 0.009178 0.42336 12.5
91 2FV5 541 0.000001989 0.58278 13.0435
92 1BKC INN 0.000006092 0.50523 13.0435
93 3DST GRG 0.02064 0.42787 13.0435
94 3D3X ARG ILE MET GLU NH2 0.009875 0.40226 13.0435
95 1HFS L04 0.0001967 0.49386 13.125
96 5OCA 9QZ 0.007011 0.44272 16.6667
97 3W68 VIV 0.005559 0.41343 16.8478
98 5G5G MCN 0.01429 0.41163 16.8478
99 1R5L VIV 0.006331 0.41414 18.4783
100 1COY AND 0.04461 0.40269 21.1957
101 1G27 BB1 0.000000000001097 0.8048 47.619
102 1RL4 BRR 0.000000001109 0.6142 49.4565
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