Receptor
PDB id Resolution Class Description Source Keywords
2AIE 1.7 Å EC: 3.5.1.88 S.PNEUMONIAE POLYPEPTIDE DEFORMYLASE COMPLEXED WITH SB- 505684 STREPTOCOCCUS PNEUMONIAE HYDROLASE
Ref.: STRUCTURAL VARIATION AND INHIBITOR BINDING IN POLYPEPTIDE DEFORMYLASE FROM FOUR DIFFERENT BACTERIAL SPECIES PROTEIN SCI. V. 12 349 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NI P:502;
 Part of Protein;
 none;
 submit data
58.693 Ni [Ni+2...
SB9 P:501;
 Valid;
 none;
 ic50 = 2.2 uM
194.23 C10 H14 N2 O2 Cc1cc...
SO4 P:3001;
 Invalid;
 none;
 submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4EOX 1.78 Å EC: 3.5.1.88 X-RAY STRUCTURE OF POLYPEPTIDE DEFORMYLASE BOUND TO A ACYLPR INHIBITOR STREPTOCOCCUS PNEUMONIAE ALPHA-BETA PEPTIDE DEFORMYLASE METAL ION BINDING HYDROLASEHYDROLASE INHIBITOR COMPLEX
Ref.: ACYLPROLINAMIDES: A NEW CLASS OF PEPTIDE DEFORMYLAS INHIBITORS WITH IN VIVO ANTIBACTERIAL ACTIVITY. BIOORG.MED.CHEM.LETT. V. 22 4028 2012
Members (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 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 6OW7 ic50 = 1 nM N9Y C20 H29 N5 O4 c1ccnc(c1)....
7 4EOX ic50 = 0.28 nM 0S5 C22 H29 N3 O5 c1ccc(cc1)....
8 6OW2 ic50 = 3 nM NB4 C22 H36 F N7 O4 Cc1nc(c(c(....
9 3STR Ki = 334 nM 3LI C28 H33 Cl N10 O4 S Cc1cccc(c1....
70% Homology Family (22)
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 6OW7 ic50 = 1 nM N9Y C20 H29 N5 O4 c1ccnc(c1)....
7 4EOX ic50 = 0.28 nM 0S5 C22 H29 N3 O5 c1ccc(cc1)....
8 6OW2 ic50 = 3 nM NB4 C22 H36 F N7 O4 Cc1nc(c(c(....
9 3STR Ki = 334 nM 3LI C28 H33 Cl N10 O4 S Cc1cccc(c1....
10 3G6N - MET ALA SER n/a n/a
11 2OKL - BB2 C19 H35 N3 O5 CCCCC[C@H]....
12 1LQY - BB2 C19 H35 N3 O5 CCCCC[C@H]....
13 5JF3 Ki = 38 nM SF5 C18 H23 N3 O5 CCCC[C@H](....
14 5JEZ - MET ALA SER n/a n/a
15 5JF7 Ki = 909 nM 6JU C17 H15 Br N2 O2 c1ccc(cc1)....
16 5JF2 Ki = 13 nM SF7 C16 H20 F N3 O3 CCCC[C@H](....
17 5JF5 Ki = 63 nM 7JT C19 H23 N3 O5 c1cc2c(cc1....
18 5JF0 - MET ALA ARG n/a n/a
19 5JF4 Ki = 65 nM 6JT C20 H23 N3 O4 c1ccc2c(c1....
20 5JF6 Ki = 62 nM BB4 C10 H9 Br N2 O2 c1cc2c(cc1....
21 5JF1 Ki = 64 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
22 5JF8 Ki = 1428 nM PN3 C15 H22 N2 O4 CC(C)(C)OC....
50% Homology Family (23)
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 6OW7 ic50 = 1 nM N9Y C20 H29 N5 O4 c1ccnc(c1)....
7 4EOX ic50 = 0.28 nM 0S5 C22 H29 N3 O5 c1ccc(cc1)....
8 6OW2 ic50 = 3 nM NB4 C22 H36 F N7 O4 Cc1nc(c(c(....
9 3STR Ki = 334 nM 3LI C28 H33 Cl N10 O4 S Cc1cccc(c1....
10 3G6N - MET ALA SER n/a n/a
11 2OKL - BB2 C19 H35 N3 O5 CCCCC[C@H]....
12 1Q1Y - BB2 C19 H35 N3 O5 CCCCC[C@H]....
13 1LQY - BB2 C19 H35 N3 O5 CCCCC[C@H]....
14 5JF3 Ki = 38 nM SF5 C18 H23 N3 O5 CCCC[C@H](....
15 5JEZ - MET ALA SER n/a n/a
16 5JF7 Ki = 909 nM 6JU C17 H15 Br N2 O2 c1ccc(cc1)....
17 5JF2 Ki = 13 nM SF7 C16 H20 F N3 O3 CCCC[C@H](....
18 5JF5 Ki = 63 nM 7JT C19 H23 N3 O5 c1cc2c(cc1....
19 5JF0 - MET ALA ARG n/a n/a
20 5JF4 Ki = 65 nM 6JT C20 H23 N3 O4 c1ccc2c(c1....
21 5JF6 Ki = 62 nM BB4 C10 H9 Br N2 O2 c1cc2c(cc1....
22 5JF1 Ki = 64 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
23 5JF8 Ki = 1428 nM PN3 C15 H22 N2 O4 CC(C)(C)OC....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: SB9; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 SB9 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: SB9; Similar ligands found: 140
No: Ligand Similarity coefficient
1 SB7 0.9636
2 OJD 0.9365
3 GNW 0.9278
4 KPV 0.9213
5 1PS 0.9199
6 HAR 0.9188
7 JFM 0.9157
8 IJ1 0.9143
9 0V7 0.9132
10 JKK 0.9116
11 DHC 0.9100
12 6HN 0.9096
13 0V8 0.9089
14 ZIP 0.9083
15 0XR 0.9072
16 ZEZ 0.9057
17 C9M 0.9053
18 ARG 0.9052
19 11X 0.9045
20 GGB 0.9028
21 KYN 0.9027
22 6Q3 0.9023
23 5PV 0.9021
24 API 0.9016
25 TZP 0.9010
26 DAR 0.8999
27 I2E 0.8996
28 D53 0.8971
29 D4G 0.8965
30 WA2 0.8960
31 XI7 0.8951
32 IJ4 0.8949
33 ASE 0.8942
34 P1J 0.8940
35 848 0.8940
36 6J5 0.8939
37 4JK 0.8933
38 3IP 0.8931
39 ZYC 0.8930
40 7HV 0.8910
41 5KJ 0.8894
42 1HR 0.8891
43 D8I 0.8882
44 5WN 0.8880
45 2MR 0.8874
46 Z70 0.8869
47 JX7 0.8856
48 PLP 0.8855
49 3XH 0.8853
50 WT2 0.8846
51 ILO 0.8842
52 S8G 0.8839
53 DHH 0.8834
54 FZ3 0.8824
55 EEK 0.8823
56 PBN 0.8820
57 3KJ 0.8819
58 5TO 0.8818
59 BSA 0.8814
60 ALY 0.8811
61 JCQ 0.8809
62 3H2 0.8803
63 PLR 0.8798
64 TOH 0.8795
65 E9S 0.8793
66 BZM 0.8782
67 DA2 0.8776
68 AHL 0.8770
69 4Z1 0.8767
70 HL6 0.8757
71 6C5 0.8756
72 CIR 0.8753
73 VIO 0.8749
74 8CV 0.8747
75 JOV 0.8746
76 3IB 0.8746
77 XRS 0.8744
78 D8Q 0.8739
79 NK5 0.8736
80 NMM 0.8736
81 SNR 0.8734
82 27K 0.8733
83 1YO 0.8727
84 NFZ 0.8724
85 3D3 0.8724
86 A51 0.8722
87 4TB 0.8722
88 JM2 0.8721
89 DTB 0.8713
90 TB8 0.8712
91 J9Y 0.8708
92 P2L 0.8704
93 TPM 0.8703
94 S0B 0.8703
95 2E6 0.8697
96 MLY 0.8696
97 C0H 0.8696
98 EXY 0.8695
99 6C9 0.8691
100 SX2 0.8688
101 HRG 0.8688
102 0OO 0.8687
103 T03 0.8682
104 EGV 0.8682
105 37E 0.8681
106 FY8 0.8680
107 NRG 0.8680
108 QH3 0.8679
109 RA7 0.8671
110 N9M 0.8670
111 6C4 0.8666
112 JF5 0.8657
113 IPL 0.8651
114 C4F 0.8642
115 6N4 0.8635
116 IPO 0.8635
117 GZV 0.8634
118 7VY 0.8631
119 9J6 0.8629
120 LPB 0.8629
121 PLP PMP 0.8627
122 26P 0.8623
123 LZ5 0.8618
124 00G 0.8614
125 MUK 0.8607
126 M3L 0.8607
127 F63 0.8606
128 6L6 0.8591
129 4ZD 0.8589
130 2JJ 0.8584
131 6FG 0.8583
132 XRX 0.8579
133 QME 0.8575
134 LVP 0.8573
135 531 0.8569
136 EN1 0.8562
137 LVD 0.8539
138 GHQ 0.8537
139 IAG 0.8536
140 RGP 0.8532
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4EOX; Ligand: 0S5; Similar sites found with APoc: 5
This union binding pocket(no: 1) in the query (biounit: 4eox.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 1G27 BB1 38.6905
2 1G27 BB1 38.6905
3 1G27 BB1 38.6905
4 1RL4 BRR 49.4681
5 1RL4 BRR 49.4681
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