Receptor
PDB id Resolution Class Description Source Keywords
6PAU 1.93 Å EC: 2.3.1.97 STRUCTURE OF HUMAN NMT2 WITH MYRISTOYL-LYSINE PEPTIDE AND CO HOMO SAPIENS LYSINE MYRISTOYL MYRISTOYLATION N-MYRISTOYL TRANSFERASE TRANSFERASE
Ref.: NMT1 AND NMT2 ARE LYSINE MYRISTOYLTRANSFERASES REGU THE ARF6 GTPASE CYCLE. NAT COMMUN V. 11 1067 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:502;
A:509;
A:505;
A:507;
A:508;
A:503;
A:506;
A:510;
A:504;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
4PS A:511;
 Valid;
 none;
 submit data
438.328 C11 H24 N2 O10 P2 S CC(C)...
MG A:501;
 Part of Protein;
 none;
 submit data
24.305 Mg [Mg+2...
LYS VAL LEU SER LYS ILE PHE MYR C:3;
 Valid;
 none;
 submit data
1046.45 n/a O=C([...
SO4 A:512;
 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
6PAU 1.93 Å EC: 2.3.1.97 STRUCTURE OF HUMAN NMT2 WITH MYRISTOYL-LYSINE PEPTIDE AND CO HOMO SAPIENS LYSINE MYRISTOYL MYRISTOYLATION N-MYRISTOYL TRANSFERASE TRANSFERASE
Ref.: NMT1 AND NMT2 ARE LYSINE MYRISTOYLTRANSFERASES REGU THE ARF6 GTPASE CYCLE. NAT COMMUN V. 11 1067 2020
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 4C2X - NHW C36 H64 N7 O17 P3 S CCCCCCCCCC....
2 6PAU - 4PS C11 H24 N2 O10 P2 S CC(C)(CO[P....
70% Homology Family (39)
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 = 4.74 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 Ki = 1.73 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 6QRM - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
24 4C2Y - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
25 6SK2 - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
26 4C2Z ic50 = 17 nM 646 C21 H24 Cl2 N6 O2 S Cc1c(c(n(n....
27 6FZ3 - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
28 6SJZ - ACE GLY ASN CYS PHE SER LYS PRO ARG n/a n/a
29 5O6H ic50 = 0.013 uM 9M2 C24 H28 F N5 O Cc1c(c(n(n....
30 6FZ2 - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
31 5O9V - GLY GLY CYS PHE SER LYS PRO LYS MYR n/a n/a
32 5O9U - GLY CYS SER VAL SER LYS LYS LYS MYR n/a n/a
33 6SK8 - GLY ASP CYS PHE SER LYS PRO ARG n/a n/a
34 6F56 - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
35 5O6J ic50 = 4.6 nM 9M8 C25 H30 F N5 O Cc1c(c(n(n....
36 5O9T - 1IP CYS PHE SER LYS PRO ARG n/a n/a
37 5MU6 Kd < 210 pM KFK C25 H29 F2 N5 O Cc1c(c(n(n....
38 4C2X - NHW C36 H64 N7 O17 P3 S CCCCCCCCCC....
39 6PAU - 4PS C11 H24 N2 O10 P2 S CC(C)(CO[P....
50% Homology Family (90)
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 = 4.74 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 Ki = 1.73 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 6QDH - HZ8 C18 H27 N5 CCN(C)c1c2....
29 6QDA ic50 = 0.24 uM HWZ C19 H26 N6 CN1CCC(CC1....
30 4CYP - A62 C21 H23 Cl2 N O3 c1cc(ccc1C....
31 6QDG - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
32 4UCM Kd = 180 uM X6W C12 H15 N3 CNCc1cc(nn....
33 5G21 - YN4 C25 H27 N5 O3 S CCOC(=O)c1....
34 6GNS - F65 C30 H43 N3 O4 S CN1CCC(CC1....
35 4CYQ Ki = 59 nM YAU C29 H29 Cl2 F N2 O4 c1cc(ccc1C....
36 6QDD - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
37 4CGP - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
38 6GNT - F5Q C29 H38 N4 O2 S CN1CCC(CC1....
39 2WUU ic50 = 68.7 nM NHW C36 H64 N7 O17 P3 S CCCCCCCCCC....
40 5AG6 - 5PE C16 H16 N2 O3 S COc1cc(ccc....
41 4CGL ic50 = 0.031 uM A6K C21 H24 Cl2 N2 O2 c1cc(ccc1C....
42 6QDC ic50 = 0.62 uM HXE C18 H26 N6 S CCN1CCC(CC....
43 5AGE - M9M C23 H31 N3 O3 Cc1cc(no1)....
44 6GNU - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
45 6EU5 Ki = 2 nM BXN C23 H33 Cl2 N5 O2 S Cc1c(c(n(n....
46 5A27 Ki = 0.02 uM TUT C21 H24 Cl N3 O3 [H]/N=C(Cc....
47 6QD9 ic50 = 2.7 uM HWT C16 H24 N6 S CN(C)CCCN(....
48 6QDE - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
49 4A32 - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
50 4C7H - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
51 6QDB - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
52 4UCN - JRB C10 H15 N3 c1ccc(c(c1....
53 4C7I - JJ1 C27 H52 N4 O5 C1CCC(CC1)....
54 6GNV - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
55 4CGN ic50 = 0.55 uM 7AH C21 H22 F N3 O c1cc(ccc1C....
56 5AG4 - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
57 5G20 - QBY C23 H24 N2 O3 S CCSc1c2cc(....
58 6EWF - 31A C21 H25 N3 O3 [H]/N=C(Cc....
59 4A30 - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
60 4CGM ic50 = 1.02 uM CWZ C27 H28 N4 S c1cc(cc(c1....
61 4A31 - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
62 5A28 Ki = 0.01 uM TUQ C20 H24 Cl N5 O2 Cc1c(c(n(n....
63 6QDF ic50 = 1.2 uM HWN C20 H32 N6 S CC(C)(C)C1....
64 4CGO ic50 = 0.299 uM 6KV C17 H24 N6 S CN1CCC(CC1....
65 4CYN Ki = 1406 nM A6M C21 H24 Cl2 N2 O2 c1cc(ccc1C....
66 6GNH - F4T C21 H26 N2 O5 S COc1ccc(cc....
67 6FZ5 Ki = 430 nM BXN C23 H33 Cl2 N5 O2 S Cc1c(c(n(n....
68 6QRM - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
69 4C2Y - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
70 6SK2 - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
71 4C2Z ic50 = 17 nM 646 C21 H24 Cl2 N6 O2 S Cc1c(c(n(n....
72 6FZ3 - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
73 6SJZ - ACE GLY ASN CYS PHE SER LYS PRO ARG n/a n/a
74 5O6H ic50 = 0.013 uM 9M2 C24 H28 F N5 O Cc1c(c(n(n....
75 6FZ2 - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
76 5O9V - GLY GLY CYS PHE SER LYS PRO LYS MYR n/a n/a
77 5O9U - GLY CYS SER VAL SER LYS LYS LYS MYR n/a n/a
78 6SK8 - GLY ASP CYS PHE SER LYS PRO ARG n/a n/a
79 6F56 - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
80 5O6J ic50 = 4.6 nM 9M8 C25 H30 F N5 O Cc1c(c(n(n....
81 5O9T - 1IP CYS PHE SER LYS PRO ARG n/a n/a
82 5MU6 Kd < 210 pM KFK C25 H29 F2 N5 O Cc1c(c(n(n....
83 4C2X - NHW C36 H64 N7 O17 P3 S CCCCCCCCCC....
84 6PAU - 4PS C11 H24 N2 O10 P2 S CC(C)(CO[P....
85 4QBJ - 2XQ C25 H23 F3 N2 O3 Cc1c(oc2c1....
86 4UWJ - 7L5 C21 H28 Cl2 F2 N4 O2 S Cc1c(c(n(n....
87 4UWI - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
88 1IIC - MYA C35 H62 N7 O17 P3 S CCCCCCCCCC....
89 1IID - NHM C36 H64 N7 O17 P3 S CCCCCCCCCC....
90 1IYK Ki = 0.25 uM MIM C33 H52 N6 O4 Cc1nccn1CC....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 4PS; Similar ligands found: 20
No: Ligand ECFP6 Tc MDL keys Tc
1 4PS 1 1
2 PNS 0.783333 1
3 9EF 0.61194 0.934426
4 PNY 0.580645 0.827586
5 9Z3 0.555556 0.949153
6 H2V 0.526316 0.966667
7 N7E 0.526316 0.904762
8 JQG 0.525641 0.966102
9 PSR 0.519481 0.966667
10 PAZ 0.515152 0.881356
11 COD 0.490566 0.670588
12 SH3 0.488372 0.791667
13 COA 0.477477 0.682353
14 AFY 0.465116 0.865672
15 9Z6 0.464286 0.919355
16 OPI 0.458333 0.8
17 S2N 0.456522 0.890625
18 168 0.423077 0.786885
19 COS 0.403361 0.666667
20 0T1 0.401709 0.662791
Ligand no: 2; Ligand: LYS VAL LEU SER LYS ILE PHE MYR; Similar ligands found: 40
No: Ligand ECFP6 Tc MDL keys Tc
1 LYS VAL LEU SER LYS ILE PHE MYR 1 1
2 GLN PHE LYS ASP ASN VAL ILE LEU LEU 0.506757 0.821429
3 LYS VAL ILE THR PHE ILE ASP LEU 0.503546 0.872727
4 GLY CYS SER VAL SER LYS LYS LYS MYR 0.47482 0.909091
5 SER ILE ILE ASN PHE GLU LYS LEU 0.472603 0.890909
6 GLU ILE ILE ASN PHE GLU LYS LEU 0.465753 0.87037
7 PHE GLU ASP LEU ARG VAL LEU SER PHE 0.464052 0.758065
8 LYS VAL LEU PHE LEU ASP GLY 0.463768 0.849057
9 SER ILE ILE GLY PHE GLU LYS LEU 0.459459 0.943396
10 ACE GLY LYS SER PHE SER LYS PRO ARG MYR 0.458333 0.8125
11 SER LEU ASN TYR ILE ILE LYS VAL LYS GLU 0.458065 0.847458
12 PHE GLU ASP LEU ARG VAL SER SER PHE 0.454545 0.758065
13 SER GLU LEU GLU ILE LYS ARG TYR 0.453947 0.793651
14 GLU ASP GLU ASP PHE GLU ILE LEU SER LEU 0.450331 0.854545
15 ALA ILE PHE GLN SER SER MET THR LYS 0.450331 0.862069
16 GLY ASN CYS PHE SER LYS ARG ARG ALA ALA MYR 0.45 0.910714
17 ASP GLU LEU GLU ILE LYS ALA TYR 0.449664 0.824561
18 PHE LEU SER TYR LYS 0.449275 0.79661
19 GLY ILE LEU GLU PHE VAL PHE THR LEU 0.438356 0.821429
20 CYS THR GLU LEU LYS LEU SER ASP TYR 0.431373 0.813559
21 LYS GLN TRP LEU VAL TRP LEU PHE LEU 0.425 0.709677
22 ILE ARG LYS ILE LEU PHE LEU ASP GLY ILE 0.423313 0.813559
23 LEU PRO PHE ASP LYS SER THR ILE MET 0.421965 0.764706
24 GLU GLN TYR LYS PHE TYR SER VAL 0.416107 0.813559
25 TYR GLN SER LYS LEU 0.416058 0.842105
26 LYS GLN GLU PRO GLN GLU ILE ASP PHE 0.415663 0.730159
27 PHE LEU GLU LYS 0.413534 0.811321
28 LEU ARG ASN GLN SER VAL PHE ASN PHE 0.412903 0.734375
29 GLY GLY LYS LEU SER LYS LYS LYS LYS MYR 0.412587 0.924528
30 CYS THR PHE LYS THR LYS THR ASN 0.411348 0.807018
31 PHE GLU ASP LEU ARG LEU LEU SER PHE 0.407895 0.758065
32 GLY GLY CYS PHE SER LYS PRO LYS MYR 0.406977 0.784615
33 SER GLY ILE PHE LEU GLU THR SER 0.405594 0.836364
34 SER SER ILE GLU PHE ALA ARG LEU 0.405063 0.8
35 SER ALA ASN SER PHE THR LEU ILE GLY GLU 0.405063 0.872727
36 ARG ARG LEU ILE PHE NH2 0.404255 0.666667
37 LYS LYS SER LYS THR LYS CYS VAL ILE PHE 0.402878 0.767857
38 MET LEU ILE TYR SER MET TRP GLY LYS 0.402235 0.764706
39 MET PHE SER ILE ASP ASN ILE LEU ALA 0.401274 0.79661
40 PHE LEU SER THR LYS 0.4 0.836364
Similar Ligands (3D)
Ligand no: 1; Ligand: 4PS; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 2; Ligand: LYS VAL LEU SER LYS ILE PHE MYR; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6PAU; Ligand: 4PS; 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: 6pau.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
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