Receptor
PDB id Resolution Class Description Source Keywords
2CNX 2.1 Å EC: 2.1.1.43 WDR5 AND HISTONE H3 LYSINE 4 DIMETHYL COMPLEX AT 2.1 ANGSTROM HOMO SAPIENS HISTONE PRESENTER LYSINE METHYLATION MLL1 LEUKEMIA HOX GENE ACTIVATION TRANSCRIPTION ACTIVATION TRANSCRIPTION
Ref.: HISTONE H3 RECOGNITION AND PRESENTATION BY THE WDR5 MODULE 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 MLY GLN P:1;
Valid;
none;
submit data
632.764 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 MLY GLN; Similar ligands found: 91
No: Ligand ECFP6 Tc MDL keys Tc
1 ALA ARG THR MLY GLN 1 1
2 ALA ARG THR MLY GLN THR ALA ARG LYS TYR 0.775281 0.966667
3 ALA ARG THR MLY GLN THR ALA 0.775281 0.966667
4 ALA ARG THR MLY GLN THR ALA ARG MLY SER 0.75 0.983051
5 ALA ARG THR MLY GLN THR ALA ARG LYS 0.71134 0.966667
6 ALA ARG THR MLY GLN THR ALA ARG TYR 0.648148 0.893939
7 ALA ARG THR M3L GLN THR ALA ARG 0.646465 0.951613
8 ALA 2MR THR MLY GLN THR ALA ALA 0.634615 0.983333
9 ALA ARG THR MLZ GLN THR ALA ARG LYS 0.631068 0.916667
10 ALA ARG THR ALY GLN THR ALA 0.618557 0.85
11 ALA ARG THR M3L GLN THR ALA 2MR LYS 0.612245 0.935484
12 ALA ARG THR M3L GLN THR ALA ARG LYS SER 0.612245 0.935484
13 ALA ARG THR M3L GLN THR ALA 0.612245 0.935484
14 ALA ARG THR M3L GLN THR ALA ARG LYS 0.606061 0.935484
15 ALA ARG THR MLZ GLN THR ALA ARG LYS TYR 0.606061 0.915254
16 ALA ARG THR LYS GLN THR ALA ARG LYS SER 0.6 0.816667
17 ALA ARG THR LYS GLN THR ALA ARG 0.594059 0.816667
18 ALA ARG THR LYS GLN THR ALA ARG LYS 0.594059 0.816667
19 ALA ARG THR M3L GLN THR ALA ALA LYS ALA 0.588785 0.951613
20 ALA ARG THR MLY GLN THR ALA ARG LYS SER 0.580645 0.783333
21 THR ARG ARG GLU THR GLN LEU 0.565657 0.85
22 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.563107 0.85
23 ALA ARG MLY SER THR GLY GLY ALY 0.5625 0.951613
24 ALA ARG THR 4WQ GLN THR ALA ARG LYS SER 0.552083 0.852459
25 ARG ARG ARG GLU THR GLN VAL 0.547368 0.830508
26 GLU ALA GLN THR ARG LEU 0.538462 0.847458
27 GLU ARG THR ILE PRO ILE THR ARG GLU 0.525862 0.771429
28 PHE ALA GLY LEU ARG GLN ALA VAL THR GLN 0.523364 0.833333
29 LYS GLN THR SER VAL 0.505618 0.672131
30 ALA DA2 THR M3L GLN THR ALA ARG ALA 0.491667 0.935484
31 SAC ARG GLY THR GLN THR GLU 0.486486 0.790323
32 LEU GLY GLY ALA LYS GLN ARG GLY ASP VAL 0.485981 0.783333
33 ALA PRO ALA LEU ARG VAL VAL LYS 0.484848 0.779661
34 ALA ARG THR GLU LEU TYR ARG SER LEU 0.483333 0.761194
35 ALA ALA LEU THR ARG ALA 0.480392 0.813559
36 ALA ARG TPO LYS 0.479592 0.727273
37 LYS ALA THR LYS MLY 0.47191 0.847458
38 ALA LYS ARG HIS ARG MLY VAL LEU ARG ASP 0.471074 0.797101
39 PRO ALA THR ILE MET MET GLN ARG GLY ASN 0.468468 0.83871
40 ALA ARG 0.468354 0.661017
41 GLN ARG SER THR SEP THR 0.46789 0.731343
42 ALA ARG ALA ALA ALA ALA ALA ALA ALA 0.465909 0.711864
43 ALA THR VAL ARG THR TYR SER CYS 0.465517 0.705882
44 ALA ARG THR M3L GLN THR ALA DA2 LYS 0.465116 0.935484
45 GLN ARG ALA THR LYS MET NH2 0.463636 0.883333
46 LYS ARG ARG LYS SEP VAL 0.46 0.716418
47 ALA GLN THR ALA ARG ALY SER THR 0.456897 0.836066
48 ALA ARG M3L SER THR GLY GLY ALY 0.446281 0.921875
49 ARG HIS ARG MLY VAL LEU ARG ASP ASN 0.445312 0.811594
50 ASN ARG LEU LEU LEU THR GLY 0.444444 0.864407
51 LYS ARG LYS ARG LYS ARG LYS ARG LYS ARG 0.444444 0.7
52 LYS ARG LYS 0.438202 0.711864
53 ALA ARG MLZ SER THR GLY GLY ALY 0.438017 0.887097
54 ALA GLN PHE SER ALA SER ALA SER ARG 0.4375 0.734375
55 ACE ALA ARG THR LYS GLN 0.436893 0.813559
56 ALA ARG M3L SER 0.434343 0.857143
57 ACE GLN THR ALA ARG KCR SER THR 0.430894 0.806452
58 ARG HIS ARG MLY VAL LEU ARG ASP TYR 0.430657 0.780822
59 ASN SER THR LEU GLN 0.43 0.66129
60 ALA THR ARG ASN PHE SER GLY 0.428571 0.712121
61 ALA ASN SER ARG TRP GLN ASP THR ARG LEU 0.427481 0.71831
62 ARG ARG ARG ARG ARG ARG ARG ARG ARG ARG 0.425287 0.683333
63 ALA MET ALA PRO ARG THR LEU LEU LEU 0.425197 0.84058
64 ILE GLN GLN SER ILE GLU ARG ILE 0.424779 0.803279
65 ARG ARG ALA THR LYS MET NH2 0.423423 0.852459
66 ILE LYS ARG SER LYS LYS ASN SER LEU ALA 0.42268 0.766667
67 SER SER ARG LYS GLU TYR TYR ALA 0.419643 0.701493
68 LYS SER LEU LEU GLN GLN LEU LEU THR GLU 0.418182 0.754098
69 GLN THR ALA ARG M3L SER THR GLY 0.418033 0.920635
70 MET ABA LEU ARG MET THR ALA VAL MET 0.416667 0.868852
71 LYS ALA ALA ARG ALY SER ALA PRO ALA 0.415842 0.816667
72 ACE ALA ARG THR GLU VAL TYR NH2 0.415254 0.753846
73 ALA ILE ARG SER 0.414141 0.721311
74 GLN LEU ALA THR M3L ALA ALA ARG LYS SER 0.412698 0.935484
75 VAL THR THR ASP ILE GLN VAL LYS VAL 0.412281 0.721311
76 THR ILE MET MET GLN ARG GLY 0.412281 0.854839
77 ALA ARG LYS SEP THR GLY GLY LYS 0.409836 0.735294
78 ILE LYS ARG SER MLZ LYS ASN SER LEU ALA 0.407767 0.866667
79 ALA ASN SER ARG TRP GLN THR SER ILE ILE 0.407407 0.671233
80 MET CYS LEU ARG MET THR ALA VAL MET 0.406504 0.868852
81 GLY HIS LYS ILE LEU HIS ARG LEU LEU GLN 0.40625 0.661972
82 MET CYS LEU ARG NLE THR ALA VAL MET 0.404762 0.854839
83 GLU THR VAL ARG PHE GLN SER ASP 0.40458 0.765625
84 SER ASP TYR GLN ARG LEU 0.403509 0.738462
85 GLY GLU ARG THR ILE PRO ILE THR ARG GLU 0.403101 0.771429
86 ACE CSO ARG ALA THR LYS MET LEU 0.4 0.835821
87 LEU LYS THR LYS LEU LEU 0.4 0.728814
88 ARG GLU ARG SER PRO THR ARG 0.4 0.724638
89 LYS ARG HIS ARG MLY VAL LEU ARG ASP ASN 0.4 0.779661
90 ASN ARG LEU MET LEU THR GLY 0.4 0.854839
91 ALA ARG LYS ILE ASP ASN LEU ASP 0.4 0.777778
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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