Receptor
PDB id Resolution Class Description Source Keywords
2G99 1.9 Å EC: 2.1.1.43 STRUCTURAL BASIS FOR THE SPECIFIC RECOGNITION OF METHYLATED HISTONE H3 LYSINE 4 BY THE WD-40 PROTEIN WDR5 HOMO SAPIENS WD40 REPEAT PROTEIN STRUCTURAL PROTEIN/DNA BINDING PROTEIN COMPLEX
Ref.: STRUCTURAL BASIS FOR THE SPECIFIC RECOGNITION OF METHYLATED HISTONE H3 LYSINE 4 BY THE WD-40 PROTEIN WDR5 TO BE PUBLISHED
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ALA ARG THR MLY GLN THR ALA ARG MLY SER C:1;
D:1;
Valid;
Valid;
none;
none;
submit data
617.773 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5VFC 1.64 Å EC: 2.1.1.43 WDR5 BOUND TO INHIBITOR MM-589 HOMO SAPIENS INHIBITOR COMPLEX WD REPEAT TRANSCRIPTION TRANSCRIPTION-COMPLEX
Ref.: DISCOVERY OF A HIGHLY POTENT, CELL-PERMEABLE MACROC PEPTIDOMIMETIC (MM-589) TARGETING THE WD REPEAT DOM PROTEIN (WDR5)-MIXED LINEAGE LEUKEMIA (MLL) PROTEIN INTERACTION. J. MED. CHEM. V. 60 4818 2017
Members (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 39 families.
1 2G99 - ALA ARG THR MLY GLN THR ALA ARG MLY SER n/a n/a
2 6DAI - G2V C15 H17 N3 CN1CCc2c1c....
3 2CNX - ALA ARG THR MLY GLN n/a n/a
4 3UVM Kd = 0.03 uM GLY ALA ALA ARG ALA GLU VAL TYR LEU ARG n/a n/a
5 2H6K Kd = 8.7 uM ALA ARG THR MLZ GLN THR ALA ARG LYS n/a n/a
6 2H6Q Kd = 7.8 uM ALA ARG THR M3L GLN THR ALA ARG LYS n/a n/a
7 4Y7R Kd = 9.3 uM GLU GLU ILE ASP VAL VAL SER VAL n/a n/a
8 6DAK Ki = 7.21 uM G1Y C20 H19 N3 O c1ccc(cc1)....
9 5SXM Kd = 3 nM ACE ALA ARG THR GLU VAL TYR NH2 n/a n/a
10 3PSL - ACE ALA ARG THR LYS GLN n/a n/a
11 6D9X Ki = 323 uM FZM C12 H12 N2 c1ccc(cc1)....
12 6DAS Ki = 8.37 nM G2D C24 H25 N3 O2 Cc1ccc(cc1....
13 6DAR Ki = 0.219 uM G2J C25 H27 N3 O2 COc1cccc(c....
14 5VFC ic50 = 0.9 nM 9BA C28 H44 N8 O5 [H]/N=C(NC....
15 2H13 Kd = 4.5 uM ALA ARG THR MLY GLN THR ALA ARG LYS SER n/a n/a
16 2H6N Kd = 1.02 uM ALA ARG THR MLY GLN THR ALA ARG LYS n/a n/a
70% Homology Family (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 28 families.
1 2G99 - ALA ARG THR MLY GLN THR ALA ARG MLY SER n/a n/a
2 6DAI - G2V C15 H17 N3 CN1CCc2c1c....
3 2CNX - ALA ARG THR MLY GLN n/a n/a
4 3UVM Kd = 0.03 uM GLY ALA ALA ARG ALA GLU VAL TYR LEU ARG n/a n/a
5 2H6K Kd = 8.7 uM ALA ARG THR MLZ GLN THR ALA ARG LYS n/a n/a
6 2H6Q Kd = 7.8 uM ALA ARG THR M3L GLN THR ALA ARG LYS n/a n/a
7 4Y7R Kd = 9.3 uM GLU GLU ILE ASP VAL VAL SER VAL n/a n/a
8 6DAK Ki = 7.21 uM G1Y C20 H19 N3 O c1ccc(cc1)....
9 5SXM Kd = 3 nM ACE ALA ARG THR GLU VAL TYR NH2 n/a n/a
10 3PSL - ACE ALA ARG THR LYS GLN n/a n/a
11 6D9X Ki = 323 uM FZM C12 H12 N2 c1ccc(cc1)....
12 6DAS Ki = 8.37 nM G2D C24 H25 N3 O2 Cc1ccc(cc1....
13 6DAR Ki = 0.219 uM G2J C25 H27 N3 O2 COc1cccc(c....
14 5VFC ic50 = 0.9 nM 9BA C28 H44 N8 O5 [H]/N=C(NC....
15 2H13 Kd = 4.5 uM ALA ARG THR MLY GLN THR ALA ARG LYS SER n/a n/a
16 2H6N Kd = 1.02 uM ALA ARG THR MLY GLN THR ALA ARG LYS n/a n/a
50% Homology Family (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 2G99 - ALA ARG THR MLY GLN THR ALA ARG MLY SER n/a n/a
2 6DAI - G2V C15 H17 N3 CN1CCc2c1c....
3 2CNX - ALA ARG THR MLY GLN n/a n/a
4 3UVM Kd = 0.03 uM GLY ALA ALA ARG ALA GLU VAL TYR LEU ARG n/a n/a
5 2H6K Kd = 8.7 uM ALA ARG THR MLZ GLN THR ALA ARG LYS n/a n/a
6 2H6Q Kd = 7.8 uM ALA ARG THR M3L GLN THR ALA ARG LYS n/a n/a
7 4Y7R Kd = 9.3 uM GLU GLU ILE ASP VAL VAL SER VAL n/a n/a
8 6DAK Ki = 7.21 uM G1Y C20 H19 N3 O c1ccc(cc1)....
9 5SXM Kd = 3 nM ACE ALA ARG THR GLU VAL TYR NH2 n/a n/a
10 3PSL - ACE ALA ARG THR LYS GLN n/a n/a
11 6D9X Ki = 323 uM FZM C12 H12 N2 c1ccc(cc1)....
12 6DAS Ki = 8.37 nM G2D C24 H25 N3 O2 Cc1ccc(cc1....
13 6DAR Ki = 0.219 uM G2J C25 H27 N3 O2 COc1cccc(c....
14 5VFC ic50 = 0.9 nM 9BA C28 H44 N8 O5 [H]/N=C(NC....
15 2H13 Kd = 4.5 uM ALA ARG THR MLY GLN THR ALA ARG LYS SER n/a n/a
16 2H6N Kd = 1.02 uM ALA ARG THR MLY GLN THR ALA ARG LYS n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ALA ARG THR MLY GLN THR ALA ARG MLY SER; Similar ligands found: 78
No: Ligand ECFP6 Tc MDL keys Tc
1 ALA ARG THR MLY GLN THR ALA ARG MLY SER 1 1
2 ALA ARG THR LYS GLN THR ALA ARG 0.823529 0.844828
3 ALA ARG THR MLY GLN THR ALA ARG LYS SER 0.776471 0.79661
4 ALA ARG THR MLY GLN THR ALA 0.76087 0.983051
5 ALA ARG THR MLY GLN THR ALA ARG LYS TYR 0.76087 0.983051
6 ALA ARG THR MLY GLN THR ALA ARG LYS 0.752688 1
7 ALA ARG THR MLY GLN 0.744444 0.983051
8 ALA ARG THR LYS GLN THR ALA ARG LYS 0.621359 0.830508
9 ALA ARG THR ALY GLN THR ALA 0.6 0.864407
10 ALA ARG THR M3L GLN THR ALA 0.6 0.95082
11 ALA ARG THR M3L GLN THR ALA 2MR LYS 0.6 0.95082
12 ALA ARG THR MLZ GLN THR ALA ARG LYS 0.598131 0.915254
13 ALA ARG THR M3L GLN THR ALA ARG LYS 0.594059 0.95082
14 ALA ARG THR M3L GLN THR ALA ARG LYS SER 0.594059 0.95082
15 ALA ARG THR 4WQ GLN THR ALA ARG LYS SER 0.583333 0.866667
16 ALA ARG THR MLZ GLN THR ALA ARG LYS TYR 0.582524 0.931035
17 ARG ARG ARG GLU THR GLN VAL 0.555556 0.816667
18 ALA ARG THR MLY GLN THR ALA ARG TYR 0.555556 0.878788
19 ALA ARG 9AT 0.554217 0.793103
20 ALA 2MR THR MLY GLN THR ALA ALA 0.543689 0.983051
21 ALA ARG THR ALA ALA THR ALA ARG LYS SER 0.536082 0.779661
22 ALA ARG THR M3L GLN THR ALA ARG 0.522936 0.935484
23 ALA ILE ARG SER 0.515789 0.733333
24 ALA ARG THR M3L GLN THR ALA DA2 LYS 0.515625 0.95082
25 ACE ALA ARG THR LYS GLN 0.514852 0.827586
26 ALA ARG M3L SER 0.510417 0.870968
27 ILE LYS ARG SER LYS LYS ASN SER LEU ALA 0.510417 0.779661
28 ALA ALA LEU THR ARG ALA 0.509804 0.827586
29 ACE GLN THR ALA ARG BTK SER THR 0.508929 0.85
30 ACE GLN THR ALA ARG PRK SER THR 0.5 0.819672
31 ALA ARG THR M3L GLN THR ALA ALA LYS ALA 0.495726 0.935484
32 GLN THR ALA ARG M3L SER 0.491228 0.935484
33 ALA ARG MLY SER THR GLY GLY ALY 0.487603 0.935484
34 THR ARG ARG GLU THR GLN LEU 0.485981 0.833333
35 GLU ARG THR ILE PRO ILE THR ARG GLU 0.475 0.753623
36 THR M3L GLN 0.473118 0.819672
37 ACE GLN THR ALA ARG KCR SER THR 0.470588 0.833333
38 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.469027 0.833333
39 ALA ILE LEU HIS ARG LEU LEU GLN 0.463415 0.647059
40 ARG ARG ARG ARG ARG ARG ARG ARG ARG ARG 0.456522 0.661017
41 ARG ARG ARG ARG ARG ARG ARG ARG 0.456522 0.661017
42 GLU ALA GLN THR ARG LEU 0.45614 0.830508
43 ALA LYS ARG HIS ARG MLY VAL LEU ARG ASP 0.454545 0.75
44 GLN LEU ALA THR M3L ALA ALA ARG LYS SER 0.452174 0.934426
45 LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 0.44898 0.677966
46 ALA DA2 THR M3L GLN THR ALA ARG ALA 0.448 0.95082
47 PRO ALA THR ILE MET MET GLN ARG GLY ASN 0.447368 0.852459
48 ALA ARG LYS SEP THR GLY GLY LYS 0.443548 0.746269
49 ACE GLU ALA GLN THR ARG LEU 0.434783 0.847458
50 LYS ALA ARG VAL LEU ALA GLU ALA MET SER 0.434426 0.783333
51 LYS ALA ARG VAL LEU ALA GLU ALA MET 0.434426 0.783333
52 ALA ARG LYS ILE ASP ASN LEU ASP 0.434426 0.761905
53 GLU THR VAL ARG PHE GLN SER ASP 0.434109 0.761905
54 ALA GLN THR ALA ARG ALY SER THR 0.433333 0.85
55 PRO ALA ALA LYS ARG VAL LYS LEU ASP 0.431373 0.741379
56 ALA ARG THR GLU LEU TYR ARG SER LEU 0.429688 0.746269
57 GLN ARG ALA THR LYS MET NH2 0.428571 0.898305
58 ILE LYS ARG SER MLZ LYS ASN SER LEU ALA 0.428571 0.881356
59 ALA ARG ALA ALA ALA ALA ALA ALA ALA 0.425532 0.694915
60 ALA THR PRK ALA ALA ARG LYS SER 0.422018 0.733333
61 ALA MET ARG VAL 0.42 0.762712
62 ALA THR ARG ASN PHE SER GLY 0.418033 0.723077
63 ACE THR ARG GLU 0.417582 0.793103
64 GLN THR ALA ARG M3L SER THR GLY 0.416 0.935484
65 THR ALA ARG M3L SER THR 0.415842 0.870968
66 SAC ARG GLY THR GLN THR GLU 0.415254 0.774194
67 ARG HIS ARG MLY VAL LEU ARG ASP ASN 0.414815 0.797101
68 ALA THR VAL ARG THR TYR SER CYS 0.414634 0.691176
69 LYS ARG HIS ARG MLY VAL LEU ARG ASP ASN 0.413043 0.810345
70 ALA PRO ALA LEU ARG VAL VAL LYS 0.412844 0.762712
71 ARG ARG ALA THR LYS MET NH2 0.410256 0.866667
72 ASN ARG LEU ILE LEU THR GLY 0.409091 0.75
73 PHE ALA GLY LEU ARG GLN ALA VAL THR GLN 0.408333 0.816667
74 LEU GLY GLY ALA LYS GLN ARG GLY ASP VAL 0.40678 0.766667
75 GLU ALY ARG 0.40566 0.762712
76 ARG HIS ARG MLY VAL LEU ARG ASP TYR 0.405594 0.767123
77 ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP 0.4 0.656716
78 ASN ARG LEU LEU LEU THR GLY 0.4 0.830508
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5VFC; Ligand: 9BA; 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: 5vfc.bio1) has 34 residues
No: Leader PDB Ligand Sequence Similarity
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