Receptor
PDB id Resolution Class Description Source Keywords
5JF2 2 Å EC: 3.5.1.88 CRYSTAL STRUCTURE OF TYPE 2 PDF FROM STREPTOCOCCUS AGALACTIA COMPLEX WITH INHIBITOR AT002 STREPTOCOCCUS AGALACTIAE PDF TYPE 2 NME N-TERMINAL METHIONINE EXCISION STREPTOCOCAGALACTIAE INHIBITOR AT002 HYDROLASE
Ref.: A UNIQUE PEPTIDE DEFORMYLASE PLATFORM TO RATIONALLY AND CHALLENGE NOVEL ACTIVE COMPOUNDS. SCI REP V. 6 35429 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN A:310;
A:308;
A:306;
A:311;
A:307;
A:304;
A:305;
A:309;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
IMD A:303;
Invalid;
none;
submit data
69.085 C3 H5 N2 c1c[n...
ACT A:302;
Invalid;
none;
submit data
59.044 C2 H3 O2 CC(=O...
SF7 A:301;
Valid;
Atoms found LESS than expected: % Diff = 0.348;
Ki = 13 nM
321.347 C16 H20 F N3 O3 CCCC[...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5JF2 2 Å EC: 3.5.1.88 CRYSTAL STRUCTURE OF TYPE 2 PDF FROM STREPTOCOCCUS AGALACTIA COMPLEX WITH INHIBITOR AT002 STREPTOCOCCUS AGALACTIAE PDF TYPE 2 NME N-TERMINAL METHIONINE EXCISION STREPTOCOCAGALACTIAE INHIBITOR AT002 HYDROLASE
Ref.: A UNIQUE PEPTIDE DEFORMYLASE PLATFORM TO RATIONALLY AND CHALLENGE NOVEL ACTIVE COMPOUNDS. SCI REP V. 6 35429 2016
Members (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 5JF3 Ki = 38 nM SF5 C18 H23 N3 O5 CCCC[C@H](....
2 5JEZ - MET ALA SER n/a n/a
3 5JF7 Ki = 909 nM 6JU C17 H15 Br N2 O2 c1ccc(cc1)....
4 5JF2 Ki = 13 nM SF7 C16 H20 F N3 O3 CCCC[C@H](....
5 5JF5 Ki = 63 nM 7JT C19 H23 N3 O5 c1cc2c(cc1....
6 5JF0 - MET ALA ARG n/a n/a
7 5JF4 Ki = 65 nM 6JT C20 H23 N3 O4 c1ccc2c(c1....
8 5JF6 Ki = 62 nM BB4 C10 H9 Br N2 O2 c1cc2c(cc1....
9 5JF1 Ki = 64 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
10 5JF8 Ki = 1428 nM PN3 C15 H22 N2 O4 CC(C)(C)OC....
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: SF7; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 SF7 1 1
2 SF5 0.736842 0.835821
3 7JT 0.40404 0.742857
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5JF2; Ligand: SF7; Similar sites found: 74
This union binding pocket(no: 1) in the query (biounit: 5jf2.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2O4N TPV 0.004633 0.4182 None
2 2QZT PLM 0.007639 0.41139 None
3 3GGU 017 0.008011 0.41046 None
4 5UC9 MYR 0.01332 0.41004 None
5 4XCP PLM 0.01802 0.40968 None
6 3U7S 017 0.009995 0.40186 None
7 1BWO LPC 0.005658 0.40413 2.22222
8 4RW3 TDA 0.002279 0.45087 2.45098
9 3GKJ HC3 0.004425 0.41064 2.45098
10 1XON PIL 0.01149 0.40342 2.45098
11 1KUK PCA LYS TRP 0.00002764 0.47345 2.46305
12 4WKI 3PW 0.00001635 0.47804 2.94118
13 1MMQ RRS 0.0001941 0.47196 2.94118
14 2ZXG S23 0.001162 0.44489 2.94118
15 4GAA BES 0.0007386 0.42933 2.94118
16 4ARF IP8 GLY PRO ALA 0.005793 0.42775 2.94118
17 4MGA 27L 0.01867 0.41054 2.94118
18 2X5W K2B 0.0108 0.40185 2.94118
19 1YP1 LYS ASN LEU 0.000006931 0.46396 2.9703
20 2W14 WR2 0.0002082 0.44517 2.9703
21 3KP6 SAL 0.0002871 0.51589 3.31126
22 2FV5 541 0.00001111 0.54224 3.43137
23 1BKC INN 0.0000368 0.46549 3.43137
24 4KX8 L2O VAL VAL ASP 0.001404 0.4322 3.43137
25 3KRO DST 0.004104 0.42055 3.43137
26 3KRO IPE 0.004104 0.42055 3.43137
27 4QOM PYG 0.002943 0.41831 3.43137
28 4AR8 IP8 GLY PRO ALA 0.001484 0.41715 3.43137
29 2YB9 HA0 0.02551 0.41576 3.43137
30 2TCL RO4 0.0001424 0.47513 3.5503
31 5CSD ACD 0.01474 0.40986 3.77358
32 4Q5M ROC 0.003578 0.43029 3.94089
33 4ZBY URA 0.01696 0.41547 4.12371
34 3ZVS MLI 0.0004454 0.4122 4.375
35 1R55 097 0.00003179 0.45385 4.41176
36 2ZCQ B65 0.01851 0.40891 4.41176
37 1ATL 0QI 0.00003375 0.50678 4.45545
38 3R1V AZB 0.007492 0.40741 4.72441
39 2V57 PRL 0.01157 0.41897 4.73684
40 1Q3A NGH 0.000004671 0.48346 4.84848
41 4WZV E40 0.0001941 0.47751 5
42 1RM8 BAT 0.00003361 0.44431 5.32544
43 4DD8 BAT 0.00001139 0.45454 5.39216
44 2XXP DSL 0.02596 0.41712 5.39216
45 4GK9 MAN BMA MAN MAN MAN 0.0133 0.40507 5.39216
46 1RQJ RIS 0.008585 0.40479 5.88235
47 1IDA 0PO 0.003655 0.43479 6.06061
48 3HY9 098 0.00001989 0.5095 6.86275
49 3Q2H QHF 0.00006167 0.48841 6.86275
50 4DV8 0LX 0.001017 0.45912 6.86275
51 4BXK 1IU 0.003205 0.43857 6.86275
52 5OCA 9QZ 0.01519 0.41481 6.86275
53 4NJS G08 0.007173 0.41656 7.07071
54 5T2Z 017 0.008544 0.41055 7.07071
55 5IKH 6BW 0.007145 0.41787 7.35294
56 5V4R MGT 0.0005156 0.49821 7.40741
57 4CA5 3EF 0.002183 0.45836 7.84314
58 3C88 ARG ARG GLY CYS NH2 0.02016 0.40966 7.84314
59 1ZVX FIN 0.0004092 0.47725 7.97546
60 3R9V DXC 0.01326 0.41714 8.33333
61 2FXU ATP 0.02889 0.41063 8.82353
62 4UCC ZKW 0.0233 0.40446 9.31373
63 4B6C B5U 0.006989 0.40018 9.69388
64 2J83 BAT 0.00007821 0.48637 10.2941
65 3WV1 WHH 0.000791 0.47242 11.1111
66 4ZW3 4S9 0.0006869 0.46693 12.7451
67 2VCX GSH 0.02977 0.4053 13.5678
68 2VCX D26 0.02977 0.4053 13.5678
69 1FBL HTA 0.002882 0.43455 14.7059
70 3HBV ALA LYS ALA SER GLN ALA ALA 0.001505 0.40635 18.1373
71 1HN4 MJI 0.009944 0.43604 20.6107
72 2DYR PGV 0.02148 0.40023 26.5306
73 1G27 BB1 0.000000001031 0.69341 38.0952
74 1RL4 BRR 0.000000041 0.54541 49.4681
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