Receptor
PDB id Resolution Class Description Source Keywords
2H13 1.58 Å EC: 2.1.1.43 CRYSTAL STRUCTURE OF WDR5/HISTONE H3 COMPLEX HOMO SAPIENS HISTONE BETA-PROPELLER WD40-REPEAT MLL TRANSCRIPTION
Ref.: MOLECULAR RECOGNITION OF HISTONE H3 BY THE WD40 PROTEIN WDR5. NAT.STRUCT.MOL.BIOL. V. 13 698 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ALA ARG THR MLY GLN THR ALA ARG LYS SER B:1;
Valid;
none;
Kd = 4.5 uM
545.642 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 (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 MLY GLN THR ALA ARG LYS SER; Similar ligands found: 76
No: Ligand ECFP6 Tc MDL keys Tc
1 ALA ARG THR MLY GLN THR ALA ARG LYS SER 1 1
2 ALA ARG THR MLY GLN THR ALA ARG MLY SER 0.77381 0.79661
3 ALA ARG THR LYS GLN THR ALA ARG LYS 0.625 0.921569
4 ALA ARG THR LYS GLN THR ALA ARG 0.625 0.921569
5 ALA ARG THR ALY GLN THR ALA 0.617021 0.886792
6 ALA ARG THR MLZ GLN THR ALA ARG LYS TYR 0.604167 0.854545
7 ALA ARG THR MLY GLN THR ALA ARG LYS 0.594059 0.783333
8 ALA ARG THR M3L GLN THR ALA 2MR LYS 0.59375 0.758065
9 ALA ARG THR MLY GLN THR ALA ARG LYS TYR 0.59375 0.783333
10 ALA ARG THR MLY GLN THR ALA 0.59375 0.783333
11 ALA ARG THR M3L GLN THR ALA 0.59375 0.758065
12 ALA ARG THR M3L GLN THR ALA ARG LYS SER 0.59375 0.758065
13 ALA ARG THR M3L GLN THR ALA ARG LYS 0.587629 0.758065
14 ALA ARG THR 4WQ GLN THR ALA ARG LYS SER 0.582418 0.821429
15 ALA ARG THR LYS GLN THR ALA ARG LYS SER 0.581633 0.921569
16 ALA ARG THR MLY GLN 0.580645 0.783333
17 ACE ALA ARG THR LYS GLN 0.537634 0.92
18 ALA ILE ARG SER 0.534091 0.88
19 ILE LYS ARG SER LYS LYS ASN SER LEU ALA 0.528736 0.862745
20 ALA ALA LEU THR ARG ALA 0.520833 0.92
21 ALA ARG THR M3L GLN THR ALA ARG 0.519231 0.746032
22 ARG ARG ARG GLU THR GLN VAL 0.510638 0.94
23 ALA ARG THR MLZ GLN THR ALA ARG LYS 0.509259 0.824561
24 ALA ARG THR M3L GLN THR ALA ALA LYS ALA 0.5 0.746032
25 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.5 0.886792
26 ALA ARG THR M3L GLN THR ALA DA2 LYS 0.495935 0.758065
27 ALA ARG M3L SER 0.48913 0.68254
28 THR ARG ARG GLU THR GLN LEU 0.485149 0.886792
29 PRO ALA THR ILE MET MET GLN ARG GLY ASN 0.476636 0.872727
30 LYS GLN THR SER VAL 0.465909 0.75
31 ALA TYR ARG 0.462366 0.777778
32 GLU ALA GLN THR ARG LEU 0.462264 0.921569
33 ALA MET ARG VAL 0.461538 0.740741
34 ARG ARG ARG ARG ARG ARG ARG ARG 0.458824 0.76
35 ALA ARG ALA ALA ALA ALA ALA ALA ALA 0.458824 0.836735
36 PRO ALA ALA LYS ARG VAL LYS LEU ASP 0.456522 0.784314
37 ALA ARG LYS ILE ASP ASN LEU ASP 0.455357 0.803571
38 GLN LEU ALA THR M3L ALA ALA ARG LYS SER 0.453782 0.758065
39 LYS ALA ALA ARG ALY SER ALA PRO ALA 0.452632 0.849057
40 ALA GLN THR ALA ARG ALY SER THR 0.451327 0.87037
41 LYS ALA ARG VAL LEU ALA GLU ALA MET SER 0.451327 0.763636
42 LYS ALA ARG VAL LEU ALA GLU ALA MET 0.451327 0.763636
43 GLN ARG SER THR SEP THR 0.448598 0.810345
44 ALA THR VAL ARG THR TYR SER CYS 0.447368 0.779661
45 GLU THR VAL ARG PHE GLN SER ASP 0.443548 0.854545
46 ALA ARG TPO LYS 0.443299 0.745763
47 ILE LYS ARG SER MLZ LYS ASN SER LEU ALA 0.443299 0.803571
48 ALA ARG LYS SEP THR GLY GLY LYS 0.439655 0.783333
49 ALA DA2 THR M3L GLN THR ALA ARG ALA 0.438017 0.758065
50 ASN ARG LEU LEU LEU THR GLY 0.4375 0.903846
51 ALA 2MR THR MLY GLN THR ALA ALA 0.434783 0.770492
52 ALA THR ARG ASN PHE SER GLY 0.434783 0.854545
53 ALA PRO ALA LEU ARG VAL VAL LYS 0.434343 0.773585
54 GLU ARG THR ILE PRO ILE THR ARG GLU 0.433333 0.738462
55 ALA ILE GLU THR ASA 0.431579 0.72549
56 GLN ARG ALA THR LYS MET NH2 0.431193 0.854545
57 ALA ARG THR MLY GLN THR ALA ARG TYR 0.429752 0.701493
58 SAC ARG GLY THR GLN THR GLU 0.428571 0.886792
59 THR M3L GLN 0.428571 0.655738
60 LYS ARG LYS ARG LYS ARG LYS ARG 0.428571 0.745098
61 ACE GLN THR ALA ARG KCR SER THR 0.425 0.87037
62 PHE ALA GLY LEU ARG GLN ALA VAL THR GLN 0.423423 0.903846
63 ASN ARG LEU ILE LEU THR GLY 0.423077 0.843137
64 ALA ARG 0.423077 0.77551
65 ALA THR PRK ALA ALA ARG LYS SER 0.421569 0.788462
66 ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP 0.421488 0.68254
67 ACE ALA ARG THR GLU VAL TYR NH2 0.421053 0.839286
68 ARG GLU ARG SER PRO THR ARG 0.419048 0.6875
69 ALA ARG THR GLU LEU TYR ARG SER LEU 0.418033 0.783333
70 LEU GLY GLY ALA LYS GLN ARG GLY ASP VAL 0.412844 0.811321
71 GLN THR ALA ARG M3L SER THR GLY 0.411765 0.746032
72 MET ABA LEU ARG MET THR ALA VAL MET 0.410256 0.839286
73 LYS ARG ARG LYS SEP VAL 0.41 0.704918
74 GLU ALY ARG 0.40625 0.773585
75 ARG ARG ALA THR LYS MET NH2 0.40367 0.821429
76 SER ARG LYS ILE ASP ASN LEU ASP 0.4 0.824561
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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