Receptor
PDB id Resolution Class Description Source Keywords
1Q1Y 1.9 Å EC: 3.5.1.88 CRYSTAL STRUCTURES OF PEPTIDE DEFORMYLASE FROM STAPHYLOCOCCU COMPLEXED WITH ACTINONIN STAPHYLOCOCCUS AUREUS METALLO-ENZYME PEPTIDE DEFORMYLASE ACTINONIN STAPHYLOCOCCAUREUS HYDROLASE
Ref.: CRYSTAL STRUCTURE OF PEPTIDE DEFORMYLASE FROM STAPH AUREUS IN COMPLEX WITH ACTINONIN, A NATURALLY OCCUR ANTIBACTERIAL AGENT PROTEINS V. 57 639 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BB2 A:301;
Valid;
none;
submit data
385.498 C19 H35 N3 O5 CCCCC...
ZN A:350;
Part of Protein;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1Q1Y 1.9 Å EC: 3.5.1.88 CRYSTAL STRUCTURES OF PEPTIDE DEFORMYLASE FROM STAPHYLOCOCCU COMPLEXED WITH ACTINONIN STAPHYLOCOCCUS AUREUS METALLO-ENZYME PEPTIDE DEFORMYLASE ACTINONIN STAPHYLOCOCCAUREUS HYDROLASE
Ref.: CRYSTAL STRUCTURE OF PEPTIDE DEFORMYLASE FROM STAPH AUREUS IN COMPLEX WITH ACTINONIN, A NATURALLY OCCUR ANTIBACTERIAL AGENT PROTEINS V. 57 639 2004
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 1Q1Y - 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 1Q1Y - BB2 C19 H35 N3 O5 CCCCC[C@H]....
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 : 1Q1Y; Ligand: BB2; Similar sites found: 138
This union binding pocket(no: 1) in the query (biounit: 1q1y.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3KO0 TFP 0.001517 0.46965 None
2 3KP6 SAL 0.002174 0.46049 None
3 2ALG DAO 0.00466 0.42292 None
4 2ALG HP6 0.004661 0.42291 None
5 2I0D MUT 0.04691 0.41035 None
6 1UO5 PIH 0.03849 0.40523 None
7 5T2Z 017 0.02056 0.40277 None
8 1FBL HTA 0.00003292 0.49248 1.57068
9 2VCX D26 0.02571 0.41759 1.57068
10 2VCX GSH 0.02571 0.41759 1.57068
11 4ZOM 4Q3 0.04756 0.41386 1.57068
12 3SP6 IL2 0.006444 0.4127 1.57068
13 5X40 ACP 0.01012 0.4089 1.57068
14 4UCC ZKW 0.01907 0.40619 1.57068
15 3ET1 ET1 0.01172 0.40073 1.57068
16 5EXA 5SO 0.01575 0.40056 1.57068
17 1KUK PCA LYS TRP 0.00001301 0.51874 2.09424
18 2J83 BAT 0.00005158 0.51143 2.09424
19 4QHP 32Q 0.005433 0.41981 2.09424
20 3KC1 2T6 0.01094 0.4021 2.09424
21 3EYK EYK 0.02167 0.41765 2.32558
22 1RM8 BAT 0.00004071 0.53417 2.36686
23 3G2Y GF4 0.005829 0.43585 2.6178
24 3CV6 NAP 0.02569 0.40773 2.6178
25 3CV6 HXS 0.02681 0.40773 2.6178
26 3V1S 0LH 0.0188 0.40576 2.6178
27 5UC9 MYR 0.01487 0.40177 2.6178
28 4B7P 9UN 0.04267 0.40173 2.6178
29 2OUA AES 0.01461 0.41232 2.65957
30 2Z9I GLY ALA THR VAL 0.003553 0.44795 2.77778
31 5V4R MGT 0.0005681 0.49098 3.08642
32 4WZV E40 0.0001211 0.50271 3.125
33 2YB9 HA0 0.009983 0.44638 3.14136
34 3GKJ HC3 0.002702 0.43203 3.14136
35 1UOU CMU 0.005734 0.40877 3.14136
36 4I90 CHT 0.01654 0.40655 3.14136
37 3WCA FPS 0.02237 0.40099 3.14136
38 5CSD ACD 0.01791 0.41255 3.14465
39 1R55 097 0.00002417 0.5373 3.66492
40 4AR8 IP8 GLY PRO ALA 0.0004679 0.46034 3.66492
41 4QOM PYG 0.001632 0.44215 3.66492
42 3ET3 ET1 0.005168 0.41901 3.66492
43 2QCS ANP 0.01108 0.41163 3.66492
44 4ZVI 4S4 0.008416 0.40736 3.66492
45 5IKH 6BW 0.02304 0.4039 3.66492
46 4F4S EFO 0.01371 0.40799 3.94737
47 4AIG FLX 0.00001365 0.5414 4.18848
48 4RW3 TDA 0.001601 0.47165 4.18848
49 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 0.00276 0.46613 4.18848
50 3B9Z CO2 0.0039 0.4531 4.18848
51 4MRP GSH 0.003644 0.44909 4.18848
52 3HBV ALA LYS ALA SER GLN ALA ALA 0.00236 0.43072 4.18848
53 5KDS A2G THR ALA PRO GLY GLY NAG SIA 0.005667 0.4112 4.18848
54 2OBD PCW 0.02151 0.40303 4.18848
55 4ZBR DIF 0.02417 0.40289 4.18848
56 5GK9 ACO 0.02031 0.40044 4.18848
57 3HY9 098 0.00001324 0.5361 4.71204
58 4ARF IP8 GLY PRO ALA 0.0003134 0.46823 4.71204
59 1VPD TLA 0.01021 0.41593 4.71204
60 1UWK NAD 0.03809 0.40505 4.71204
61 4CZG QH3 0.028 0.40293 4.71204
62 3ZVS MLI 0.0003881 0.43651 5
63 1ATL 0QI 0.00001626 0.53938 5.2356
64 4WKI 3PW 0.00001148 0.5374 5.2356
65 4DD8 BAT 0.000007728 0.49284 5.2356
66 4Y2H SAH 0.02045 0.41364 5.2356
67 5LI1 ANP 0.007809 0.41248 5.2356
68 4QLX KTC 0.02784 0.40096 5.2356
69 4RVU NDP 0.02946 0.4008 5.2356
70 4B52 RDF 0.009857 0.40026 5.2356
71 3WV1 WHH 0.00035 0.50381 5.26316
72 2V57 PRL 0.01592 0.4048 5.26316
73 5B0W 22B 0.01606 0.4104 5.75916
74 5AAV GW5 0.04913 0.40434 5.75916
75 4V3I ASP LEU THR ARG PRO 0.007821 0.42715 5.83658
76 1MMQ RRS 0.0001097 0.46511 5.88235
77 2ZXG S23 0.0004745 0.47652 6.28272
78 5EW9 5VC 0.04164 0.42695 6.28272
79 4P6X HCY 0.01399 0.41451 6.28272
80 2XQ0 BES 0.001829 0.40805 6.28272
81 4BLW AMP 0.03029 0.40021 6.28272
82 2QZT PLM 0.003271 0.4398 6.30631
83 1HFS L04 0.000255 0.49901 6.80628
84 4KX8 L2O VAL VAL ASP 0.0003975 0.47048 6.80628
85 4ORM FMN 0.04946 0.40912 6.80628
86 4ORM ORO 0.04946 0.40912 6.80628
87 4ORM 2V6 0.04946 0.40912 6.80628
88 3RI1 3RH 0.01432 0.40906 6.80628
89 5IR4 ZPE 0.02824 0.40839 6.80628
90 3RLF MAL 0.01246 0.40553 6.80628
91 4DV8 0LX 0.0003477 0.49527 7.32984
92 3AQT RCO 0.008831 0.42386 7.32984
93 3FHI ANP 0.01439 0.40622 7.32984
94 1XF1 CIT 0.01523 0.40285 7.32984
95 3DWB RDF 0.005732 0.40258 7.32984
96 3EWC MCF 0.01788 0.4003 7.32984
97 4RHP PEF 0.006284 0.40916 7.8534
98 5O4J PJL 0.01679 0.41177 8.37696
99 5O4J SAH 0.0212 0.40787 8.37696
100 5O4J 9KH 0.0212 0.40787 8.37696
101 2TCL RO4 0.0000828 0.50194 8.90052
102 1BKC INN 0.00004828 0.49332 8.90052
103 2FV5 541 0.00001011 0.42121 8.90052
104 3AHO 3A2 0.007952 0.41699 9.42408
105 3G58 988 0.00601 0.41632 9.42408
106 2D5Z L35 0.04771 0.4158 9.42408
107 5C2H 4XU 0.0187 0.40834 9.42408
108 5C2H 4PX 0.02567 0.40679 9.42408
109 1XMY ROL 0.01351 0.40381 9.42408
110 3FWN ATR 0.02819 0.40175 9.42408
111 3FWN 6PG 0.01315 0.40021 9.42408
112 3NFD COA 0.01246 0.40554 9.80392
113 4ZW3 4S9 0.0004432 0.49013 9.94764
114 4GAA BES 0.0004459 0.44847 9.94764
115 3W68 VIV 0.01078 0.40761 9.94764
116 4K90 MLA 0.01752 0.40578 9.94764
117 1IDA 0PO 0.009533 0.42605 10.101
118 2O4N TPV 0.01576 0.40434 10.101
119 1ZVX FIN 0.0001969 0.50733 10.4294
120 2W14 WR2 0.0001719 0.47738 10.4712
121 1Q3A NGH 0.000004055 0.57493 10.9091
122 4B6C B5U 0.005041 0.40394 10.9948
123 3R1V AZB 0.008224 0.41629 11.0236
124 3Q2H QHF 0.00004584 0.47383 12.5654
125 5OCA 9QZ 0.01278 0.41491 12.5654
126 4HY1 19X 0.01542 0.401 12.5654
127 1YP1 LYS ASN LEU 0.000003137 0.50781 14.1361
128 2VWA PTY 0.005704 0.43408 17.8218
129 3DBK RDF 0.006489 0.41256 18.3246
130 2FXU ATP 0.02348 0.42439 18.8482
131 2V5E SCR 0.00637 0.42531 22.7723
132 3N7S 3N7 0.01313 0.41338 22.9167
133 4WB6 ATP 0.009762 0.41425 24.6073
134 2Y69 CHD 0.007098 0.42453 28.3784
135 2DYR PGV 0.01246 0.42139 28.7671
136 1RL4 BRR 0.000000001846 0.75078 31.9372
137 4IN9 SER TRP PHE PRO 0.000605 0.40485 33.7349
138 1G27 BB1 0.00000000004631 0.7055 38.6905
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