Receptor
PDB id Resolution Class Description Source Keywords
2H6K 1.89 Å EC: 2.1.1.43 HISTONE H3 RECOGNITION AND PRESENTATION BY THE WDR5 MODULE O COMPLEX HOMO SAPIENS WD40 WD-REPEAT HISTONE MODIFICATION MLL SET CHROMATIN GENE REGULATION
Ref.: HISTONE H3 RECOGNITION AND PRESENTATION BY THE WDR5 OF THE MLL1 COMPLEX. NAT.STRUCT.MOL.BIOL. V. 13 704 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ALA ARG THR MLZ GLN THR ALA ARG LYS C:1;
D:1;
 Valid;
Valid;
 none;
none;
 Kd = 8.7 uM
1077.3 n/a O=C([...
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 (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 36 families.
1 2G99 - ALA ARG THR MLY GLN THR ALA ARG MLY SER n/a n/a
2 2CNX - ALA ARG THR MLY GLN n/a n/a
3 3UVM Kd = 0.03 uM GLY ALA ALA ARG ALA GLU VAL TYR LEU ARG n/a n/a
4 2H6K Kd = 8.7 uM ALA ARG THR MLZ GLN THR ALA ARG LYS n/a n/a
5 2H6Q Kd = 7.8 uM ALA ARG THR M3L GLN THR ALA ARG LYS n/a n/a
6 4Y7R Kd = 9.3 uM GLU GLU ILE ASP VAL VAL SER VAL n/a n/a
7 5SXM Kd = 3 nM ACE ALA ARG THR GLU VAL TYR NH2 n/a n/a
8 3PSL - ACE ALA ARG THR LYS GLN n/a n/a
9 5VFC ic50 = 0.9 nM 9BA C28 H44 N8 O5 [H]/N=C(NC....
10 2H13 Kd = 4.5 uM ALA ARG THR MLY GLN THR ALA ARG LYS SER n/a n/a
11 2H6N Kd = 1.02 uM ALA ARG THR MLY GLN THR ALA ARG LYS n/a n/a
70% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 26 families.
1 2G99 - ALA ARG THR MLY GLN THR ALA ARG MLY SER n/a n/a
2 2CNX - ALA ARG THR MLY GLN n/a n/a
3 3UVM Kd = 0.03 uM GLY ALA ALA ARG ALA GLU VAL TYR LEU ARG n/a n/a
4 2H6K Kd = 8.7 uM ALA ARG THR MLZ GLN THR ALA ARG LYS n/a n/a
5 2H6Q Kd = 7.8 uM ALA ARG THR M3L GLN THR ALA ARG LYS n/a n/a
6 4Y7R Kd = 9.3 uM GLU GLU ILE ASP VAL VAL SER VAL n/a n/a
7 5SXM Kd = 3 nM ACE ALA ARG THR GLU VAL TYR NH2 n/a n/a
8 3PSL - ACE ALA ARG THR LYS GLN n/a n/a
9 5VFC ic50 = 0.9 nM 9BA C28 H44 N8 O5 [H]/N=C(NC....
10 2H13 Kd = 4.5 uM ALA ARG THR MLY GLN THR ALA ARG LYS SER n/a n/a
11 2H6N Kd = 1.02 uM ALA ARG THR MLY GLN THR ALA ARG LYS n/a n/a
50% Homology Family (11)
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 2CNX - ALA ARG THR MLY GLN n/a n/a
3 3UVM Kd = 0.03 uM GLY ALA ALA ARG ALA GLU VAL TYR LEU ARG n/a n/a
4 2H6K Kd = 8.7 uM ALA ARG THR MLZ GLN THR ALA ARG LYS n/a n/a
5 2H6Q Kd = 7.8 uM ALA ARG THR M3L GLN THR ALA ARG LYS n/a n/a
6 4Y7R Kd = 9.3 uM GLU GLU ILE ASP VAL VAL SER VAL n/a n/a
7 5SXM Kd = 3 nM ACE ALA ARG THR GLU VAL TYR NH2 n/a n/a
8 3PSL - ACE ALA ARG THR LYS GLN n/a n/a
9 5VFC ic50 = 0.9 nM 9BA C28 H44 N8 O5 [H]/N=C(NC....
10 2H13 Kd = 4.5 uM ALA ARG THR MLY GLN THR ALA ARG LYS SER n/a n/a
11 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 MLZ GLN THR ALA ARG LYS; Similar ligands found: 100
No: Ligand ECFP6 Tc MDL keys Tc
1 ALA ARG THR MLZ GLN THR ALA ARG LYS 1 1
2 ALA ARG THR M3L GLN THR ALA ARG 0.737864 0.903226
3 ALA ARG THR LYS GLN THR ALA ARG LYS SER 0.72549 0.892857
4 ALA ARG THR M3L GLN THR ALA ALA LYS ALA 0.722222 0.903226
5 ALA ARG THR LYS GLN THR ALA ARG 0.718447 0.892857
6 ALA ARG THR LYS GLN THR ALA ARG LYS 0.718447 0.892857
7 ALA ARG THR MLZ GLN THR ALA ARG LYS TYR 0.699029 0.964286
8 ALA ARG THR MLY GLN 0.631068 0.916667
9 ALA ARG THR MLY GLN THR ALA ARG LYS 0.625 0.916667
10 ALA ARG THR MLY GLN THR ALA ARG TYR 0.603306 0.848485
11 GLU ALA GLN THR ARG LEU 0.585586 0.859649
12 ALA ARG THR M3L GLN THR ALA DA2 LYS 0.576923 0.887097
13 ALA ARG THR ALY GLN THR ALA 0.572727 0.928571
14 ALA DA2 THR M3L GLN THR ALA ARG ALA 0.572581 0.887097
15 ALA ARG THR MLY GLN THR ALA 0.567568 0.916667
16 ALA ARG THR M3L GLN THR ALA 0.567568 0.887097
17 ALA ARG THR M3L GLN THR ALA 2MR LYS 0.567568 0.887097
18 ALA ARG THR MLY GLN THR ALA ARG LYS TYR 0.567568 0.916667
19 ALA ARG THR M3L GLN THR ALA ARG LYS SER 0.567568 0.887097
20 ALA 2MR THR MLY GLN THR ALA ALA 0.563025 0.933333
21 ALA ARG THR M3L GLN THR ALA ARG LYS 0.5625 0.887097
22 PHE ALA GLY LEU ARG GLN ALA VAL THR GLN 0.543103 0.844828
23 THR ARG ARG GLU THR GLN LEU 0.526786 0.894737
24 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.525862 0.894737
25 GLN ARG ALA THR LYS MET NH2 0.525862 0.929825
26 ALA PRO ALA LEU ARG VAL VAL LYS 0.523364 0.789474
27 ALA GLN THR ALA ARG ALY SER THR 0.516393 0.912281
28 ALA ARG THR MLY GLN THR ALA ARG LYS SER 0.509259 0.824561
29 ALA ARG MLZ SER THR GLY GLY ALY 0.507937 0.965517
30 ALA ARG TPO LYS 0.504673 0.761905
31 ALA ARG THR MLY GLN THR ALA ARG MLY SER 0.504425 0.9
32 LEU GLY GLY ALA LYS GLN ARG GLY ASP VAL 0.495726 0.793103
33 ALA ALA LEU THR ARG ALA 0.491071 0.824561
34 ACE GLN THR ALA ARG KCR SER THR 0.488372 0.87931
35 GLN THR ALA ARG M3L SER THR GLY 0.488189 0.873016
36 ALA GLN PHE SER ALA SER ALA SER ARG 0.487395 0.8
37 ARG ARG ALA THR LYS MET NH2 0.487179 0.929825
38 ALA ARG THR 4WQ GLN THR ALA ARG LYS SER 0.486486 0.864407
39 ARG ARG ARG GLU THR GLN VAL 0.481818 0.842105
40 ILE LYS ARG SER MLZ LYS ASN SER LEU ALA 0.477064 0.912281
41 ACE CSO ARG ALA THR LYS MET LEU 0.469231 0.875
42 MET ABA LEU ARG MET THR ALA VAL MET 0.464567 0.881356
43 LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 0.46 0.767857
44 LYS ARG ARG LYS SEP VAL 0.459459 0.723077
45 GLN LEU ALA THR M3L ALA ALA ARG LYS SER 0.458647 0.887097
46 ALA ARG THR GLU LEU TYR ARG SER LEU 0.458647 0.796875
47 SER SER ARG LYS GLU TYR TYR ALA 0.458333 0.734375
48 ALA ARG MLZ SER ALA PRO ALA THR 0.458015 0.768116
49 PRO ALA THR ILE MET MET GLN ARG GLY ASN 0.455285 0.881356
50 LYS ARG LYS 0.454545 0.75
51 VAL LYS VAL VAL ALA LYS LYS TYR ARG ASN 0.451613 0.765625
52 GLU ARG THR ILE PRO ILE THR ARG GLU 0.451128 0.753623
53 ALA ARG ALA ALA ALA ALA ALA ALA ALA 0.45 0.75
54 SAC ARG GLY THR GLN THR GLU 0.448 0.862069
55 ALA LYS ALA SER GLN ALA ALA 0.445455 0.719298
56 GLY ARG PHE ALA ALA ALA ILE ALA LYS 0.445312 0.754098
57 LEU GLU LYS ALA ARG GLY SER THR TYR 0.445205 0.8
58 MET CYS LEU ARG MET THR ALA VAL MET 0.442748 0.913793
59 VAL ALA ARG SER 0.442308 0.758621
60 LYS GLN THR SER VAL 0.442308 0.706897
61 LYS SER LEU LEU GLN GLN LEU LEU THR GLU 0.433333 0.793103
62 SER ARG TYR TRP ALA ILE ARG THR ARG 0.433333 0.694444
63 ARG ASP ARG ALA ALA LYS LEU 0.432432 0.789474
64 ACE ALA ARG THR GLU VAL TYR NH2 0.429688 0.761905
65 MET CYS LEU ARG NLE THR ALA VAL MET 0.42963 0.898305
66 ALA ASN SER ARG TRP GLN ASP THR ARG LEU 0.429577 0.75
67 LYS GLN THR ALA ARG M3L SER THR GLY 0.428571 0.873016
68 ACE ALA ARG THR LYS GLN 0.426087 0.857143
69 ALA ARG LYS SEP THR GLY GLY LYS 0.424242 0.769231
70 ALA ILE PHE GLN SER SER MET THR LYS 0.423358 0.790323
71 ALA SER ASN GLU ASN ALA GLU THR MET 0.422764 0.766667
72 ALA ARG LYS LYS GLN THR 66N 6L5 0.421687 0.60241
73 ALA ASN SER ARG TRP GLN THR SER ILE ILE 0.42069 0.724638
74 ALA THR VAL ARG THR TYR SER CYS 0.419847 0.738462
75 GLN ARG SER THR SEP THR 0.419355 0.765625
76 LYS PRO VAL LEU ARG THR ALA 0.419118 0.724638
77 LYS ALA PRO ARG ALY GLN LEU ALA THR LYS 0.418919 0.768116
78 ALA ASN GLY GLY ALA SER GLY GLN VAL LYS 0.416667 0.733333
79 ILE GLN GLN SER ILE GLU ARG ILE 0.416 0.844828
80 ARG GLU ASP GLN GLU THR ALA VAL 0.415254 0.701754
81 LYS LEU VAL GLN LEU LEU THR THR THR 0.415254 0.77193
82 ALA ARG MLY SER THR GLY GLY ALY 0.414815 0.903226
83 ALA ARG M3L SER THR GLY GLY ALY 0.414815 0.875
84 LYS GLN LYS 0.414141 0.642857
85 LYS ALA ARG VAL LEU ALA GLU ALA MET SER 0.412214 0.810345
86 LYS ALA ARG VAL LEU ALA GLU ALA MET 0.412214 0.810345
87 LYS ARG GLU ALA ILE VAL LYS ALA ASP GLU 0.41129 0.672414
88 PHE GLU ALA LYS LYS LEU VAL 0.411215 0.649123
89 THR LYS THR ALA THR ILE ASN ALA SER 0.408 0.762712
90 THR PRO THR ARG ASP VAL ALA THR SER PRO 0.407407 0.714286
91 SER GLU ILE GLU PHE ALA ARG LEU 0.405797 0.774194
92 LEU LYS THR LYS LEU LEU 0.405405 0.736842
93 VAL THR THR ASP ILE GLN VAL LYS VAL 0.404762 0.758621
94 ALA ARG LYS ILE ASP ASN LEU ASP 0.40458 0.816667
95 ALA ARG 0.404255 0.696429
96 SER GLU LEU GLU ILE LYS ARG TYR 0.402878 0.784615
97 ILE LYS ARG SER LYS LYS ASN SER LEU ALA 0.4 0.807018
98 GLY HIS LYS ILE LEU HIS ARG LEU LEU GLN 0.4 0.666667
99 SER GLN LEU LYS ASN ASN ALA LYS GLU ILE 0.4 0.737705
100 THR LYS ASN TYR LYS GLN THR SER VAL 0.4 0.692308
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5VFC; Ligand: 9BA; Similar sites found: 21
This union binding pocket(no: 1) in the query (biounit: 5vfc.bio1) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5G3R 89A 0.02684 0.40437 1.60772
2 5LUN ARG 0.0282 0.40684 2.2508
3 4ZTD ALA GLY ALA GLY ALA 0.01968 0.41856 2.7668
4 2YBP 2HG 0.04273 0.40326 2.89389
5 2OS2 OGA 0.04277 0.40308 2.89389
6 1NU4 MLA 0.04572 0.42796 3.09278
7 5KJW 53C 0.03471 0.40538 3.53698
8 1OFU GDP 0.01111 0.40228 3.75
9 4K79 GAL A2G 0.01932 0.41538 4.09091
10 4K55 H6P 0.007558 0.43619 4.83871
11 2PIE GLU LEU LYS TPO GLU ARG TYR 0.02362 0.41926 5.07246
12 3M89 GSP 0.01818 0.40893 5.14469
13 1I3U RR1 0.0135 0.4116 5.51181
14 3AIH BMA MAN MAN 0.02712 0.4117 5.64516
15 4GNC ASO 0.04107 0.40402 7.02341
16 2VDF OCT 0.001732 0.42372 7.50988
17 5KQA GSH 0.03649 0.40431 8.33333
18 2ZWS PLM 0.04874 0.41784 11.5756
19 5U6D 7XG 0.0006078 0.458 21.2219
20 1Z0N BCD 0.03229 0.40388 26.0417
21 4J8B LEU LYS THR LYS LEU LEU 0.00003924 0.54682 41.8006
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