Receptor
PDB id Resolution Class Description Source Keywords
6MAY 2.05 Å EC: 2.3.1.97 CRYSTAL STRUCTURE OF N-MYRISTOYL TRANSFERASE (NMT) G386E MUT PLASMODIUM VIVAX PLASMODIUM VIVAX SSGCID GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE N- MYRISTOYLTRANSFERASE NMT PLASMODIUM VIVAX SALVADOR I STGENOMICS SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUSTRANSFERASE
Ref.: STRUCTURE-GUIDED IDENTIFICATION OF RESISTANCE BREAK ANTIMALARIAL N‐MYRISTOYLTRANSFERASE INHIBITOR CELL CHEM BIOL V. 26 991 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:504;
C:505;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
EDO C:504;
C:503;
B:503;
A:503;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
CL A:502;
B:502;
C:502;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
35.453 Cl [Cl-]
YNC A:501;
B:501;
C:501;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
973.858 C35 H58 N7 O17 P3 S CC(C)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2YNE 1.72 Å EC: 2.3.1.97 PLASMODIUM VIVAX N-MYRISTOYLTRANSFERASE IN COMPLEX WITH A BENZOTHIOPHENE INHIBITOR PLASMODIUM VIVAX TRANSFERASE MYRISTOYLATION MALARIA
Ref.: VALIDATION OF N-MYRISTOYLTRANSFERASE AS AN ANTIMALA TARGET USING AN INTEGRATED CHEMICAL BIOLOGY APPROAC NAT.CHEM. V. 6 112 2014
Members (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 4CAF Ki = 75 nM 370 C21 H23 N5 O2 S Cc1c(c(n[n....
2 4B10 - NHW C36 H64 N7 O17 P3 S CCCCCCCCCC....
3 4BBH Ki = 0.08 uM YBN C22 H23 N O4 S COc1cccc(c....
4 6MAY - YNC C35 H58 N7 O17 P3 S CC(C)(COP(....
5 2YND Ki = 32 nM 646 C21 H24 Cl2 N6 O2 S Cc1c(c(n(n....
6 5G22 Ki = 0.1 uM YN4 C25 H27 N5 O3 S CCOC(=O)c1....
7 4B11 ic50 = 2.3 uM 7I1 C26 H26 N2 O3 Cc1c2c(ccc....
8 6MB1 - JCY C25 H30 F N5 O Cc1c(c(n(n....
9 4CAE Ki = 18 nM 3F3 C23 H23 N3 O3 S COc1cccc(c....
10 5O48 - NHW C36 H64 N7 O17 P3 S CCCCCCCCCC....
11 4B12 ic50 = 10.2 uM C23 C23 H25 N O3 Cc1c2c(ccc....
12 6MB0 - JCY C25 H30 F N5 O Cc1c(c(n(n....
13 5O4V - NHW C36 H64 N7 O17 P3 S CCCCCCCCCC....
14 5G1Z Ki = 4.7 uM U53 C16 H16 N2 O3 S CCOC(=O)c1....
15 6NXG - L7Y C23 H22 Cl N3 O3 c1cc(cc(c1....
16 2YNE Ki = 2.7 nM YNE C22 H25 N5 O2 S Cc1c(c(n(n....
17 4B13 ic50 = 2 uM X25 C23 H23 N3 O3 Cc1c2c(ccc....
18 4A95 ic50 = 2.9 uM 9MT C18 H22 N2 O S CCCCc1c(nc....
19 4B14 ic50 = 0.6 uM 4XB C23 H25 N O5 Cc1c2c(ccc....
20 4C68 - EN5 C27 H53 N5 O4 C1CCC(CC1)....
21 6MAZ - 646 C21 H24 Cl2 N6 O2 S Cc1c(c(n(n....
70% Homology Family (34)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4CAF Ki = 75 nM 370 C21 H23 N5 O2 S Cc1c(c(n[n....
2 4B10 - NHW C36 H64 N7 O17 P3 S CCCCCCCCCC....
3 4BBH Ki = 0.08 uM YBN C22 H23 N O4 S COc1cccc(c....
4 6MAY - YNC C35 H58 N7 O17 P3 S CC(C)(COP(....
5 2YND Ki = 32 nM 646 C21 H24 Cl2 N6 O2 S Cc1c(c(n(n....
6 5G22 Ki = 0.1 uM YN4 C25 H27 N5 O3 S CCOC(=O)c1....
7 4B11 ic50 = 2.3 uM 7I1 C26 H26 N2 O3 Cc1c2c(ccc....
8 6MB1 - JCY C25 H30 F N5 O Cc1c(c(n(n....
9 4CAE Ki = 18 nM 3F3 C23 H23 N3 O3 S COc1cccc(c....
10 5O48 - NHW C36 H64 N7 O17 P3 S CCCCCCCCCC....
11 4B12 ic50 = 10.2 uM C23 C23 H25 N O3 Cc1c2c(ccc....
12 6MB0 - JCY C25 H30 F N5 O Cc1c(c(n(n....
13 5O4V - NHW C36 H64 N7 O17 P3 S CCCCCCCCCC....
14 5G1Z Ki = 4.7 uM U53 C16 H16 N2 O3 S CCOC(=O)c1....
15 6NXG - L7Y C23 H22 Cl N3 O3 c1cc(cc(c1....
16 2YNE Ki = 2.7 nM YNE C22 H25 N5 O2 S Cc1c(c(n(n....
17 4B13 ic50 = 2 uM X25 C23 H23 N3 O3 Cc1c2c(ccc....
18 4A95 ic50 = 2.9 uM 9MT C18 H22 N2 O S CCCCc1c(nc....
19 4B14 ic50 = 0.6 uM 4XB C23 H25 N O5 Cc1c2c(ccc....
20 4C68 - EN5 C27 H53 N5 O4 C1CCC(CC1)....
21 6MAZ - 646 C21 H24 Cl2 N6 O2 S Cc1c(c(n(n....
22 6FZ5 Ki = 430 nM BXN C23 H33 Cl2 N5 O2 S Cc1c(c(n(n....
23 4C2Y - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
24 4C2Z ic50 = 17 nM 646 C21 H24 Cl2 N6 O2 S Cc1c(c(n(n....
25 6FZ3 - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
26 5O6H ic50 = 0.013 uM 9M2 C24 H28 F N5 O Cc1c(c(n(n....
27 6FZ2 - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
28 5O9V - GLY GLY CYS PHE SER LYS PRO LYS MYR n/a n/a
29 5O9U - GLY CYS SER VAL SER LYS LYS LYS MYR n/a n/a
30 6F56 - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
31 5O6J ic50 = 4.6 nM 9M8 C25 H30 F N5 O Cc1c(c(n(n....
32 5O9T - 1IP CYS PHE SER LYS PRO ARG n/a n/a
33 5MU6 Kd < 210 pM KFK C25 H29 F2 N5 O Cc1c(c(n(n....
34 4C2X - NHW C36 H64 N7 O17 P3 S CCCCCCCCCC....
50% Homology Family (76)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4CAF Ki = 75 nM 370 C21 H23 N5 O2 S Cc1c(c(n[n....
2 4B10 - NHW C36 H64 N7 O17 P3 S CCCCCCCCCC....
3 4BBH Ki = 0.08 uM YBN C22 H23 N O4 S COc1cccc(c....
4 6MAY - YNC C35 H58 N7 O17 P3 S CC(C)(COP(....
5 2YND Ki = 32 nM 646 C21 H24 Cl2 N6 O2 S Cc1c(c(n(n....
6 5G22 Ki = 0.1 uM YN4 C25 H27 N5 O3 S CCOC(=O)c1....
7 4B11 ic50 = 2.3 uM 7I1 C26 H26 N2 O3 Cc1c2c(ccc....
8 6MB1 - JCY C25 H30 F N5 O Cc1c(c(n(n....
9 4CAE Ki = 18 nM 3F3 C23 H23 N3 O3 S COc1cccc(c....
10 5O48 - NHW C36 H64 N7 O17 P3 S CCCCCCCCCC....
11 4B12 ic50 = 10.2 uM C23 C23 H25 N O3 Cc1c2c(ccc....
12 6MB0 - JCY C25 H30 F N5 O Cc1c(c(n(n....
13 5O4V - NHW C36 H64 N7 O17 P3 S CCCCCCCCCC....
14 5G1Z Ki = 4.7 uM U53 C16 H16 N2 O3 S CCOC(=O)c1....
15 6NXG - L7Y C23 H22 Cl N3 O3 c1cc(cc(c1....
16 2YNE Ki = 2.7 nM YNE C22 H25 N5 O2 S Cc1c(c(n(n....
17 4B13 ic50 = 2 uM X25 C23 H23 N3 O3 Cc1c2c(ccc....
18 4A95 ic50 = 2.9 uM 9MT C18 H22 N2 O S CCCCc1c(nc....
19 4B14 ic50 = 0.6 uM 4XB C23 H25 N O5 Cc1c2c(ccc....
20 4C68 - EN5 C27 H53 N5 O4 C1CCC(CC1)....
21 6MAZ - 646 C21 H24 Cl2 N6 O2 S Cc1c(c(n(n....
22 5AG5 - DLR C17 H15 N3 O S c1ccc(cc1)....
23 4CYO Ki = 1.6 nM UEK C29 H30 Cl2 F N3 O3 c1cc(ccc1C....
24 2WSA Kd = 1 nM 646 C21 H24 Cl2 N6 O2 S Cc1c(c(n(n....
25 4A2Z - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
26 4UCP Kd = 200 uM 9X3 C13 H20 N2 O CNCc1cccc(....
27 4A33 - PS8 C21 H24 Cl2 N6 O2 S Cc1c(c(n(n....
28 4CYP - A62 C21 H23 Cl2 N O3 c1cc(ccc1C....
29 4UCM Kd = 180 uM X6W C12 H15 N3 CNCc1cc(nn....
30 5G21 - YN4 C25 H27 N5 O3 S CCOC(=O)c1....
31 6GNS - F65 C30 H43 N3 O4 S CN1CCC(CC1....
32 4CYQ Ki = 59 nM YAU C29 H29 Cl2 F N2 O4 c1cc(ccc1C....
33 4CGP - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
34 6GNT - F5Q C29 H38 N4 O2 S CN1CCC(CC1....
35 2WUU ic50 = 68.7 nM NHW C36 H64 N7 O17 P3 S CCCCCCCCCC....
36 5AG6 - 5PE C16 H16 N2 O3 S COc1cc(ccc....
37 4CGL ic50 = 0.031 uM A6K C21 H24 Cl2 N2 O2 c1cc(ccc1C....
38 5AGE - M9M C23 H31 N3 O3 Cc1cc(no1)....
39 6GNU - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
40 6EU5 Ki = 2 nM BXN C23 H33 Cl2 N5 O2 S Cc1c(c(n(n....
41 5A27 Ki = 0.02 uM TUT C21 H24 Cl N3 O3 [H]/N=C(Cc....
42 4A32 - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
43 4C7H - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
44 4UCN - JRB C10 H15 N3 c1ccc(c(c1....
45 4C7I - JJ1 C27 H52 N4 O5 C1CCC(CC1)....
46 6GNV - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
47 4CGN ic50 = 0.55 uM 7AH C21 H22 F N3 O c1cc(ccc1C....
48 5AG4 - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
49 5G20 - QBY C23 H24 N2 O3 S CCSc1c2cc(....
50 6EWF - 31A C21 H25 N3 O3 [H]/N=C(Cc....
51 4A30 - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
52 4CGM ic50 = 1.02 uM CWZ C27 H28 N4 S c1cc(cc(c1....
53 4A31 - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
54 5A28 Ki = 0.01 uM TUQ C20 H24 Cl N5 O2 Cc1c(c(n(n....
55 4CGO ic50 = 0.299 uM 6KV C17 H24 N6 S CN1CCC(CC1....
56 4CYN Ki = 1406 nM A6M C21 H24 Cl2 N2 O2 c1cc(ccc1C....
57 6GNH - F4T C21 H26 N2 O5 S COc1ccc(cc....
58 6FZ5 Ki = 430 nM BXN C23 H33 Cl2 N5 O2 S Cc1c(c(n(n....
59 4C2Y - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
60 4C2Z ic50 = 17 nM 646 C21 H24 Cl2 N6 O2 S Cc1c(c(n(n....
61 6FZ3 - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
62 5O6H ic50 = 0.013 uM 9M2 C24 H28 F N5 O Cc1c(c(n(n....
63 6FZ2 - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
64 5O9V - GLY GLY CYS PHE SER LYS PRO LYS MYR n/a n/a
65 5O9U - GLY CYS SER VAL SER LYS LYS LYS MYR n/a n/a
66 6F56 - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
67 5O6J ic50 = 4.6 nM 9M8 C25 H30 F N5 O Cc1c(c(n(n....
68 5O9T - 1IP CYS PHE SER LYS PRO ARG n/a n/a
69 5MU6 Kd < 210 pM KFK C25 H29 F2 N5 O Cc1c(c(n(n....
70 4C2X - NHW C36 H64 N7 O17 P3 S CCCCCCCCCC....
71 4QBJ - 2XQ C25 H23 F3 N2 O3 Cc1c(oc2c1....
72 4UWJ - 7L5 C21 H28 Cl2 F2 N4 O2 S Cc1c(c(n(n....
73 4UWI - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
74 1IIC - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
75 1IID - NHM C36 H64 N7 O17 P3 S CCCCCCCCCC....
76 1IYK Ki = 0.25 uM MIM C33 H52 N6 O4 Cc1nccn1CC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: YNC; Similar ligands found: 133
No: Ligand ECFP6 Tc MDL keys Tc
1 YNC 1 1
2 UCC 0.876812 0.945055
3 DCC 0.876812 0.945055
4 5F9 0.876812 0.945055
5 MYA 0.876812 0.945055
6 ST9 0.876812 0.945055
7 MFK 0.876812 0.945055
8 CO8 0.869565 0.945055
9 HXC 0.855072 0.945055
10 GRA 0.828571 0.966292
11 BCO 0.818841 0.966292
12 1HE 0.818841 0.945055
13 SCA 0.807143 0.966292
14 1VU 0.804348 0.955556
15 IVC 0.792857 0.977273
16 3HC 0.792857 0.977273
17 MLC 0.792857 0.966292
18 ACO 0.788321 0.955556
19 CAA 0.787234 0.977273
20 3KK 0.776978 0.966292
21 HGG 0.776224 0.966292
22 COS 0.773723 0.944444
23 CAO 0.773723 0.934066
24 OXK 0.771429 0.966292
25 FAQ 0.770833 0.966292
26 CO6 0.765957 0.966292
27 2MC 0.760563 0.945652
28 TGC 0.760274 0.955556
29 COK 0.758865 0.944444
30 HDC 0.758389 0.945055
31 YXS 0.756944 0.877551
32 YXR 0.756944 0.877551
33 FYN 0.751773 0.965909
34 IRC 0.751724 0.977273
35 CS8 0.751678 0.934783
36 COO 0.75 0.988636
37 MCA 0.75 0.955556
38 SOP 0.746479 0.944444
39 MC4 0.744828 0.935484
40 CMC 0.741259 0.944444
41 KFV 0.739726 0.886598
42 BYC 0.739726 0.966292
43 1GZ 0.739726 0.977528
44 COW 0.739726 0.955556
45 0T1 0.73913 0.94382
46 COA 0.73913 0.965909
47 DCA 0.737226 0.922222
48 30N 0.735714 0.885417
49 AMX 0.735714 0.954545
50 BCA 0.734694 0.955556
51 2NE 0.731544 0.945055
52 A1S 0.731034 0.944444
53 CMX 0.730496 0.94382
54 MRR 0.730263 0.945055
55 MRS 0.730263 0.945055
56 COF 0.727891 0.923913
57 3CP 0.727891 0.944444
58 ETB 0.724638 0.89011
59 CAJ 0.724138 0.923077
60 NHM 0.723684 0.923913
61 UOQ 0.723684 0.923913
62 NHW 0.723684 0.923913
63 0ET 0.721854 0.923913
64 2CP 0.721088 0.934066
65 8Z2 0.720779 0.956044
66 HAX 0.72028 0.923077
67 1CZ 0.72 0.955556
68 SCO 0.71831 0.94382
69 2KQ 0.716216 0.945055
70 FCX 0.713287 0.913043
71 FAM 0.713287 0.923077
72 SCD 0.712329 0.94382
73 4CA 0.711409 0.934066
74 KGP 0.710345 0.877551
75 YZS 0.710345 0.877551
76 CA6 0.710345 0.858586
77 MCD 0.710345 0.923077
78 WCA 0.705882 0.966667
79 NMX 0.705479 0.875
80 DAK 0.703226 0.956044
81 4KX 0.701299 0.956044
82 UCA 0.701219 0.945055
83 CIC 0.697368 0.944444
84 1CV 0.694805 0.966292
85 0FQ 0.69281 0.944444
86 4CO 0.69281 0.934066
87 J5H 0.692308 0.966292
88 SO5 0.691275 0.868687
89 LCV 0.691275 0.868687
90 01A 0.688312 0.904255
91 CCQ 0.686275 0.924731
92 KGJ 0.684564 0.865979
93 KGA 0.682119 0.857143
94 CA8 0.682119 0.877551
95 1HA 0.68125 0.945055
96 YE1 0.68 0.933333
97 NHQ 0.679245 0.955056
98 PLM COA 0.677419 0.913043
99 COA PLM 0.677419 0.913043
100 HFQ 0.675159 0.923913
101 F8G 0.67284 0.925532
102 01K 0.666667 0.944444
103 S0N 0.664516 0.923077
104 7L1 0.659864 0.955556
105 CA3 0.654545 0.944444
106 COT 0.652439 0.944444
107 CA5 0.64497 0.904255
108 CO7 0.636364 0.988636
109 93P 0.631579 0.934066
110 93M 0.622857 0.934066
111 COD 0.60274 0.954545
112 N9V 0.592593 0.934066
113 JBT 0.590426 0.886598
114 4BN 0.589189 0.925532
115 5TW 0.589189 0.925532
116 HMG 0.582822 0.933333
117 OXT 0.578378 0.905263
118 COA FLC 0.554839 0.932584
119 BSJ 0.534392 0.913979
120 ASP ASP ASP ILE CMC NH2 0.508197 0.902174
121 191 0.5 0.877551
122 PAP 0.496296 0.784091
123 RFC 0.47486 0.945055
124 SFC 0.47486 0.945055
125 PPS 0.47482 0.729167
126 ACE SER ASP ALY THR NH2 COA 0.469697 0.902174
127 0WD 0.453416 0.782609
128 A3P 0.451852 0.772727
129 PTJ 0.414474 0.842697
130 PUA 0.414201 0.813187
131 3AM 0.407407 0.761364
132 A22 0.402685 0.786517
133 NA7 0.401316 0.829545
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2YNE; Ligand: YNE; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2yne.bio2) has 79 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2YNE; Ligand: NHW; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2yne.bio2) has 79 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2YNE; Ligand: YNE; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 2yne.bio3) has 67 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2YNE; Ligand: NHW; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 2yne.bio3) has 67 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 2YNE; Ligand: YNE; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 2yne.bio1) has 76 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 2YNE; Ligand: NHW; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 2yne.bio1) has 76 residues
No: Leader PDB Ligand Sequence Similarity
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