Receptor
PDB id Resolution Class Description Source Keywords
3SVJ 1.55 Å EC: 3.5.1.88 STREP PEPTIDE DEFORMYLASE WITH A TIME DEPENDENT THIAZOLIDINE STREPTOCOCCUS PNEUMONIAE ALPHA-BETA PEPTIDE DEFORMYLASE METAL BINDING PROTEIN HYDRHYDROLASE INHIBITOR COMPLEX
Ref.: UNDERSTANDING THE ORIGINS OF TIME-DEPENDENT INHIBIT POLYPEPTIDE DEFORMYLASE INHIBITORS. BIOCHEMISTRY V. 50 6642 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
4LI P:207;
Valid;
none;
Ki = 117 nM
582.12 C27 H32 Cl N9 O2 S Cc1cc...
GOL P:209;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NI P:208;
Part of Protein;
none;
submit data
58.693 Ni [Ni+2...
SO4 P:204;
P:205;
P:206;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3SVJ 1.55 Å EC: 3.5.1.88 STREP PEPTIDE DEFORMYLASE WITH A TIME DEPENDENT THIAZOLIDINE STREPTOCOCCUS PNEUMONIAE ALPHA-BETA PEPTIDE DEFORMYLASE METAL BINDING PROTEIN HYDRHYDROLASE INHIBITOR COMPLEX
Ref.: UNDERSTANDING THE ORIGINS OF TIME-DEPENDENT INHIBIT POLYPEPTIDE DEFORMYLASE INHIBITORS. BIOCHEMISTRY V. 50 6642 2011
Members (7)
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 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....
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: 4LI; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 4LI 1 1
2 3LI 0.816514 0.821429
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3SVJ; Ligand: 4LI; Similar sites found: 116
This union binding pocket(no: 1) in the query (biounit: 3svj.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5UGW GSH 0.001127 0.50466 None
2 4XCP PLM 0.0245 0.40593 None
3 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 0.01839 0.41489 1.47783
4 1YP1 LYS ASN LEU 0.000007477 0.5849 1.48515
5 3Q2H QHF 0.00006172 0.49311 1.97044
6 1KUK PCA LYS TRP 0.00002258 0.4569 1.97044
7 3HP9 CF1 0.01103 0.42938 1.97044
8 3R9V DXC 0.01397 0.41954 1.97044
9 4GK9 MAN BMA MAN MAN MAN 0.01407 0.40655 1.97044
10 1SBR VIB 0.02464 0.40422 2
11 1BWO LPC 0.004916 0.41049 2.22222
12 3AQT RCO 0.00914 0.43318 2.46305
13 1UI0 URA 0.008982 0.43239 2.46305
14 3G58 988 0.005131 0.4296 2.46305
15 5HCN DAO 0.008313 0.4286 2.46305
16 4RW3 TDA 0.004319 0.42335 2.46305
17 5CHR 4NC 0.004263 0.44567 2.91971
18 1MMQ RRS 0.0003347 0.46592 2.94118
19 4GAA BES 0.0005979 0.45941 2.95567
20 4ARF IP8 GLY PRO ALA 0.0006548 0.45762 2.95567
21 2XQ0 BES 0.004281 0.43827 2.95567
22 2V5E SCR 0.01714 0.42992 3
23 4B6C B5U 0.007135 0.40344 3.06122
24 5V4R MGT 0.0004007 0.5093 3.08642
25 3NFD COA 0.004189 0.43874 3.26797
26 3KCG NTP 0.009597 0.4207 3.38983
27 4WKI 3PW 0.00001834 0.54149 3.44828
28 1BKC INN 0.00006112 0.51665 3.44828
29 2FV5 541 0.00002625 0.43905 3.44828
30 1VPD TLA 0.00753 0.43576 3.44828
31 1OFZ FUC 0.009018 0.43054 3.44828
32 4V3I ASP LEU THR ARG PRO 0.01065 0.42962 3.44828
33 1XMY ROL 0.007913 0.4249 3.44828
34 4UCC ZKW 0.02021 0.41192 3.44828
35 1XM4 PIL 0.01094 0.40947 3.44828
36 2YFB SIN 0.04984 0.40284 3.44828
37 4QGE 35O 0.004213 0.40002 3.44828
38 1RM8 BAT 0.00007913 0.53235 3.5503
39 1JGS SAL 0.002386 0.41407 3.62319
40 3B9Z CO2 0.004846 0.46189 3.94089
41 2Z9I GLY ALA THR VAL 0.004231 0.45664 3.94089
42 1ZPD CIT 0.0067 0.43792 3.94089
43 5UC9 MYR 0.01311 0.4139 3.94089
44 2UW1 GVM 0.02153 0.40857 3.94089
45 1XF1 CIT 0.02141 0.40563 3.94089
46 5TVI MYR 0.01583 0.41876 4.34783
47 5TVI O8N 0.02764 0.41356 4.34783
48 3ZVS MLI 0.0007715 0.4743 4.375
49 4WZV E40 0.0006241 0.42255 4.375
50 1R55 097 0.00003803 0.54077 4.4335
51 4AR8 IP8 GLY PRO ALA 0.00136 0.44322 4.4335
52 3VPD CIT 0.003684 0.43268 4.4335
53 4KX8 L2O VAL VAL ASP 0.00167 0.42704 4.4335
54 2V57 PRL 0.01473 0.41747 4.73684
55 1UUY PPI 0.00525 0.41894 4.79042
56 5C1M OLC 0.003206 0.45412 4.92611
57 1UOU CMU 0.006853 0.41512 4.92611
58 3CHT 4NB 0.02157 0.41293 4.92611
59 3HW5 AMP 0.03172 0.40159 4.92611
60 4UMJ BFQ 0.02512 0.40063 4.92611
61 2W14 WR2 0.000238 0.48292 4.9505
62 3SQP 3J8 0.02093 0.41222 5.02092
63 5XNA SHV 0.03146 0.40647 5.07246
64 3HBV ALA LYS ALA SER GLN ALA ALA 0.00175 0.4474 5.41872
65 4DD8 BAT 0.00001594 0.43121 5.41872
66 5BXA MAN 0.02306 0.41047 5.41872
67 3GXO MQA 0.0167 0.40861 5.41872
68 5EXA 5SO 0.02009 0.40456 5.41872
69 2GBB CIT 0.01164 0.4165 5.76923
70 1UO4 PIH 0.004273 0.46073 5.88235
71 2IDO TMP 0.0196 0.40975 5.91398
72 3KO0 TFP 0.002772 0.46275 5.94059
73 4B52 RDF 0.01176 0.40418 6.40394
74 4ZBY URA 0.0174 0.41675 6.70103
75 3HY9 098 0.00002148 0.51303 6.89655
76 2J83 BAT 0.0001822 0.46798 6.89655
77 5KDS A2G THR ALA PRO GLY GLY NAG SIA 0.005827 0.4145 6.89655
78 2X1L MET 0.02648 0.40048 6.89655
79 4LBP 1WG 0.01765 0.40739 7
80 3NJQ NJQ 0.02487 0.40401 7.25389
81 4IA6 EIC 0.009342 0.43311 7.38916
82 5OCA 9QZ 0.01171 0.42954 7.38916
83 3A8H TAY 0.02328 0.40813 7.38916
84 4AIG FLX 0.00001973 0.54726 7.46269
85 3DWB RDF 0.006401 0.42058 7.88177
86 2XYA 7L4 0.03723 0.40491 8.24176
87 1FBL HTA 0.00006329 0.52261 8.37438
88 3O01 DXC 0.00057 0.51571 8.37438
89 2ZWI C5P 0.01019 0.41503 8.37438
90 4WBD CIT 0.03249 0.40716 8.37438
91 1ELW GLY PRO THR ILE GLU GLU VAL ASP 0.009023 0.41347 8.47458
92 5EY0 GTP 0.01808 0.40282 8.86699
93 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 0.0158 0.4057 9.52381
94 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 0.01679 0.42039 9.85222
95 2ZXG S23 0.001441 0.40209 9.85222
96 1ATL 0QI 0.00008192 0.48013 9.90099
97 2TCL RO4 0.0003557 0.45562 10.0592
98 4IN9 SER TRP PHE PRO 0.002286 0.45893 10.241
99 1ZGA HMK 0.01613 0.4014 10.3448
100 2VWA PTY 0.004283 0.45412 10.8911
101 4QOM PYG 0.003091 0.41565 11.8227
102 3EYK EYK 0.02239 0.43336 12.3153
103 1N8V BDD 0.01482 0.40316 12.5
104 1Q3A NGH 0.00001007 0.56959 13.3333
105 3N7S 3N7 0.01412 0.42179 13.5417
106 3G2Y GF4 0.02123 0.40731 14.2857
107 4F4S EFO 0.01312 0.41839 14.4737
108 2CBO TH2 0.02257 0.4065 17.3913
109 5KD8 TNR 0.01386 0.41715 17.734
110 5W97 CHD 0.01842 0.41165 21.4286
111 2Y69 CHD 0.01193 0.41963 21.7054
112 3RLF MAL 0.009279 0.42143 24.6305
113 5A86 D7E 0.01414 0.41224 29.4118
114 1G27 BB1 0.00000000007816 0.74929 38.0952
115 4MGA 27L 0.01915 0.41324 38.4615
116 1RL4 BRR 0.000000002963 0.75935 48.9362
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