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 (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 MLY SER; Similar ligands found: 75
No: Ligand ECFP6 Tc MDL keys Tc
1 ALA ARG THR MLY GLN THR ALA ARG MLY SER 1 1
2 ALA ARG THR MLY GLN THR ALA ARG LYS SER 0.77381 0.79661
3 ALA ARG THR MLY GLN THR ALA 0.758242 0.983051
4 ALA ARG THR MLY GLN THR ALA ARG LYS TYR 0.758242 0.983051
5 ALA ARG THR MLY GLN THR ALA ARG LYS 0.75 0.983051
6 ALA ARG THR MLY GLN 0.75 0.983051
7 ALA ARG THR LYS GLN THR ALA ARG LYS 0.63 0.830508
8 ALA ARG THR LYS GLN THR ALA ARG 0.63 0.830508
9 ALA ARG THR ALY GLN THR ALA 0.606061 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 M3L GLN THR ALA ARG LYS SER 0.6 0.95082
13 ALA ARG THR M3L GLN THR ALA ARG LYS 0.594059 0.95082
14 ALA ARG THR MLZ GLN THR ALA ARG LYS TYR 0.594059 0.931035
15 ALA ARG THR 4WQ GLN THR ALA ARG LYS SER 0.589474 0.866667
16 ALA ARG THR LYS GLN THR ALA ARG LYS SER 0.588235 0.830508
17 ALA 2MR THR MLY GLN THR ALA ALA 0.563636 0.966667
18 ALA ARG THR MLY GLN THR ALA ARG TYR 0.551724 0.878788
19 ALA ARG THR M3L GLN THR ALA ARG 0.527778 0.935484
20 ALA ARG THR M3L GLN THR ALA ALA LYS ALA 0.522124 0.935484
21 ALA ARG THR M3L GLN THR ALA DA2 LYS 0.515873 0.95082
22 ACE ALA ARG THR LYS GLN 0.515152 0.827586
23 ALA ALA LEU THR ARG ALA 0.514852 0.827586
24 ALA ILE ARG SER 0.510638 0.733333
25 ILE LYS ARG SER LYS LYS ASN SER LEU ALA 0.505376 0.779661
26 ALA ARG THR MLZ GLN THR ALA ARG LYS 0.504425 0.9
27 ALA ARG M3L SER 0.5 0.870968
28 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.495413 0.833333
29 ARG ARG ARG GLU THR GLN VAL 0.49 0.813559
30 GLN LEU ALA THR M3L ALA ALA ARG LYS SER 0.487603 0.95082
31 ALA ARG MLY SER THR GLY GLY ALY 0.487395 0.935484
32 THR ARG ARG GLU THR GLN LEU 0.481132 0.833333
33 GLU ALA GLN THR ARG LEU 0.459459 0.830508
34 ALA GLN THR ALA ARG ALY SER THR 0.449153 0.85
35 ALA DA2 THR M3L GLN THR ALA ARG ALA 0.448 0.95082
36 PRO ALA THR ILE MET MET GLN ARG GLY ASN 0.447368 0.852459
37 GLN ARG ALA THR LYS MET NH2 0.442478 0.898305
38 LYS ARG LYS ARG LYS ARG LYS ARG 0.442105 0.677966
39 THR M3L GLN 0.442105 0.819672
40 ALA ARG LYS ILE ASP ASN LEU ASP 0.440678 0.761905
41 SAC ARG GLY THR GLN THR GLU 0.439655 0.774194
42 ARG ARG ARG ARG ARG ARG ARG ARG 0.43956 0.661017
43 ALA ARG ALA ALA ALA ALA ALA ALA ALA 0.43956 0.694915
44 ALA ARG LYS SEP THR GLY GLY LYS 0.438017 0.746269
45 LYS ALA ALA ARG ALY SER ALA PRO ALA 0.435644 0.830508
46 ALA THR PRK ALA ALA ARG LYS SER 0.433962 0.716667
47 GLU ARG THR ILE PRO ILE THR ARG GLU 0.432 0.757143
48 LYS GLN THR SER VAL 0.431579 0.655738
49 ALA TYR ARG 0.43 0.65625
50 ALA LYS ARG HIS ARG MLY VAL LEU ARG ASP 0.428571 0.782609
51 ALA ARG THR GLU LEU TYR ARG SER LEU 0.428571 0.746269
52 ALA ARG TPO LYS 0.427184 0.712121
53 ILE LYS ARG SER MLZ LYS ASN SER LEU ALA 0.427184 0.881356
54 LYS ALA ARG VAL LEU ALA GLU ALA MET SER 0.425 0.783333
55 LYS ALA ARG VAL LEU ALA GLU ALA MET 0.425 0.783333
56 PRO ALA ALA LYS ARG VAL LYS LEU ASP 0.424242 0.741379
57 ACE GLN THR ALA ARG KCR SER THR 0.424 0.819672
58 ASN ARG LEU LEU LEU THR GLY 0.421569 0.847458
59 ALA THR VAL ARG THR TYR SER CYS 0.421488 0.691176
60 ALA THR ARG ASN PHE SER GLY 0.421488 0.723077
61 GLN ARG SER THR SEP THR 0.421053 0.716418
62 ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP 0.420635 0.681159
63 GLU THR VAL ARG PHE GLN SER ASP 0.419847 0.75
64 ALA PRO ALA LEU ARG VAL VAL LYS 0.419048 0.762712
65 ARG ARG ALA THR LYS MET NH2 0.415929 0.866667
66 ALA MET ARG VAL 0.414141 0.762712
67 LEU GLY GLY ALA LYS GLN ARG GLY ASP VAL 0.412281 0.766667
68 GLN THR ALA ARG M3L SER THR GLY 0.41129 0.935484
69 LYS ARG ARG LYS SEP VAL 0.409524 0.701493
70 LYS ARG HIS ARG MLY VAL LEU ARG ASP ASN 0.406593 0.793103
71 ARG HIS ARG MLY VAL LEU ARG ASP ASN 0.406015 0.797101
72 THR ALA ARG M3L SER THR 0.405941 0.870968
73 GLU ALY ARG 0.405941 0.762712
74 ALA ILE GLU THR ASA 0.401961 0.606557
75 ALA ASN SER ARG TRP ALY THR SER ILE ILE 0.401408 0.684932
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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