Receptor
PDB id Resolution Class Description Source Keywords
3UVM 1.57 Å EC: 2.1.1.43 CRYSTAL STRUCTURE OF WDR5 IN COMPLEX WITH THE WDR5-INTERACTI OF MLL4 HOMO SAPIENS TRITHORAX CHROMATIN BIOLOGY BETA-PROPELLER SCAFFOLDING HH3 NUCLEUS TRANSCRIPTION
Ref.: THE PLASTICITY OF WDR5 PEPTIDE-BINDING CLEFT ENABLE BINDING OF THE SET1 FAMILY OF HISTONE METHYLTRANSFE NUCLEIC ACIDS RES. V. 40 4237 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GLY ALA ALA ARG ALA GLU VAL TYR LEU ARG B:2508;
Valid;
none;
Kd = 0.03 uM
1091.28 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: GLY ALA ALA ARG ALA GLU VAL TYR LEU ARG; Similar ligands found: 116
No: Ligand ECFP6 Tc MDL keys Tc
1 GLY ALA ALA ARG ALA GLU VAL TYR LEU ARG 1 1
2 HIS GLY ALA ALA ARG ALA GLU VAL HIS LEU 0.621849 0.803571
3 LYS ALA ARG VAL LEU ALA GLU ALA MET SER 0.576923 0.75
4 LYS ALA ARG VAL LEU ALA GLU ALA MET 0.576923 0.75
5 GLY ASP GLU VAL LYS VAL PHE ARG 0.57037 0.813559
6 ARG VAL ALA GLN LEU GLU GLN VAL TYR ILE 0.564286 0.929825
7 LEU TYR LEU VAL CYS GLY GLU ARG VAL 0.56338 0.898305
8 ACE ALA ARG THR GLU VAL TYR NH2 0.561538 0.881356
9 ALA ARG THR GLU LEU TYR ARG SER LEU 0.550725 0.916667
10 SER SER LEU GLU ASN PHE ARG ALA TYR VAL 0.549669 0.857143
11 LEU TYR LEU VAL CYS GLY GLU ARG GLY 0.545455 0.898305
12 ARG PRO GLY ASN PHE LEU GLN ASN ARG PRO 0.544118 0.766667
13 PHE LEU ARG GLY ARG ALA TYR VAL LEU 0.530612 0.915254
14 ALA ALA SER LEU TYR GLU LYS LYS ALA ALA 0.529851 0.770492
15 SER SER ARG LYS GLU TYR TYR ALA 0.523438 0.881356
16 ARG ARG ILE TYR ASP LEU ILE GLU LEU 0.520833 0.948276
17 LEU TYR LEU VAL CYS GLY GLU ARG GLY PHE 0.513158 0.868852
18 LEU GLU LYS ALA ARG GLY SER THR TYR 0.509804 0.887097
19 GLU VAL TYR GLU SER 0.508065 0.741379
20 SER GLU LEU GLU ILE LYS ARG TYR 0.503497 0.870968
21 ALA TYR ARG 0.5 0.857143
22 ASP SEP TYR GLU VAL LEU ASP LEU 0.496599 0.681818
23 GLU LEU LYS TPO GLU ARG TYR 0.496552 0.833333
24 PHE TYR ARG ALA LEU MET 0.492958 0.83871
25 PHE ARG SER LYS GLY GLU GLU LEU PHE THR 0.486842 0.83871
26 ASN ALA LEU LEU ARG TYR LEU LEU ASP 0.484375 0.724138
27 THR PHE GLN ALA PSA LEU ARG GLU 0.483871 0.809524
28 GLU LEU LYS ARG LYS MET ILE TYR MET 0.483221 0.870968
29 ALA THR VAL ARG THR TYR SER CYS 0.482014 0.852459
30 VAL LYS VAL VAL ALA LYS LYS TYR ARG ASN 0.481481 0.883333
31 ARG VAL LEU PHE GLU ALA MET 0.479452 0.803279
32 TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 0.47651 0.916667
33 SER GLU ILE GLU PHE ALA ARG LEU 0.475862 0.803279
34 SER GLU ASP GLU PHE TYR ASP ALA LEU SER 0.475862 0.754098
35 ASP GLU LEU GLU ILE LYS ALA TYR 0.475524 0.779661
36 GLU LEU ARG ARG LYS MET MET TYR MET 0.475177 0.901639
37 ARG GLY TYR VAL TYR GLN GLY LEU 0.472222 0.898305
38 GLU GLU ASN LEU LEU ASP PHE VAL ARG PHE 0.469799 0.819672
39 ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP 0.468966 0.78125
40 ALA GLU THR PHE TYR VAL ASP GLY 0.467153 0.688525
41 SER SER LEU GLU ASN PHE ALA ALA TYR VAL 0.466667 0.730159
42 SER SER ILE GLU PHE ALA ARG LEU 0.466216 0.819672
43 GLN LEU ALA THR M3L ALA ALA ARG LYS SER 0.465753 0.720588
44 PHQ LEU VAL ARG TYR 0.465278 0.868852
45 GLU VAL ALA PRO PRO GLU TYR HIS ARG LYS 0.463277 0.774648
46 GLY LEU TYR ALA SER LYS LEU ALA 0.462687 0.725806
47 SER ASP TYR GLN ARG LEU 0.462687 0.929825
48 GLU GLU TYR LEU GLN ALA PHE THR TYR 0.462585 0.721311
49 ASP ALA GLU PHE ARG HIS ASP SER 0.462585 0.734375
50 PHE LEU ARG GLY ARG ALA TYR GLY LEU 0.462585 0.915254
51 GLY GLY ARG LYS LYS TYR LYS LEU 0.459854 0.931035
52 GLY GLY LYS LYS LYS TYR ARG LEU 0.459854 0.931035
53 GLY GLY LYS LYS ARG TYR LYS LEU 0.459854 0.931035
54 ARG HIS ARG MLY VAL LEU ARG ASP TYR 0.459119 0.788732
55 PHE ARG TYR LEU GLY 0.456522 0.898305
56 ALA ARG THR MLY GLN THR ALA ARG TYR 0.455782 0.848485
57 GLU LEU ASN ARG LYS MET ILE TYR MET 0.455696 0.830769
58 GLY ALA GLU VAL PHE TYR VAL ASP GLY ALA 0.454545 0.75
59 GLY VAL TYR ASP GLY ARG GLU HIS THR VAL 0.453416 0.80597
60 ASP LEU TYR CYS TYR GLU GLN LEU ASN 0.450704 0.758065
61 THR TYR PHE ALA VAL LEU MET VAL SER 0.450331 0.636364
62 GLU THR VAL ARG PHE GLN SER ASP 0.447368 0.833333
63 PHE ALA GLY LEU ARG GLN ALA VAL THR GLN 0.442029 0.783333
64 LEU PRO PHE GLU ARG ALA THR VAL MET 0.441176 0.68
65 VAL ALA PHE ARG SER 0.440298 0.793103
66 ILE LEU ALA LYS PHE LEU HIS ARG LEU 0.43949 0.723077
67 ALA ARG THR LYS GLN THR ALA ARG 0.437956 0.766667
68 ALA ARG THR LYS GLN THR ALA ARG LYS 0.437956 0.766667
69 ARG GLY TYR LEU TYR GLN GLY LEU 0.4375 0.898305
70 GLY ALA GLU THR PHE TYR VAL ASP GLY ALA 0.436242 0.741935
71 SER ARG ILE ARG ILE ARG GLY TYR VAL ARG 0.436242 0.887097
72 PTR LEU ARG VAL ALA 0.435714 0.825397
73 ARG HIS ARG MLZ VAL LEU ARG ASP ASN TYR 0.433735 0.811594
74 SER LEU ASN TYR ILE ILE LYS VAL LYS GLU 0.432258 0.777778
75 THR ASN GLU TYR LYS VAL 0.42963 0.762712
76 GLU LEU ASP LYS TYR ALA SER 0.429577 0.783333
77 PRO VAL LYS ARG ARG LEU ASP LEU GLU 0.42953 0.761905
78 LYS ALA VAL TYR ASN LEU ALA THR MET 0.428571 0.723077
79 ALA THR ALA ALA ALA THR GLU ALA TYR 0.428571 0.694915
80 GLY ILE LEU GLU PHE VAL PHE THR LEU 0.427586 0.66129
81 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.427536 0.830508
82 SER LEU PHE ASN THR VAL ALA THR LEU TYR 0.424837 0.68254
83 ARG TYR GLY PHE VAL ALA ASN PHE 0.424837 0.83871
84 ALA ARG THR MLY GLN THR ALA ARG LYS 0.422535 0.742424
85 TYR HIS SEP VAL VAL ARG TYR ALA 0.42236 0.702703
86 ASP ALA ASP GLU TYR LEU 0.422222 0.754386
87 GLY ASN PHE LEU GLN SER ARG 0.421769 0.806452
88 GLU GLU TYR LEU LYS ALA TRP THR PHE 0.421687 0.676471
89 GLY ALA ARG ALA HIS SER SER 0.421429 0.757576
90 ASP ARG VAL GLU LEU ASN ALA PRO ARG GLN 0.419355 0.676056
91 SER LEU TYR LEU THR VAL ALA THR LEU 0.417266 0.7
92 GLY SER HIS LEU GLU VAL GLN GLY TYR TRP 0.417143 0.7
93 VAL LEU ARG ASP ASP LEU LEU GLU ALA 0.416667 0.824561
94 ALA ALA LEU THR ARG ALA 0.416667 0.762712
95 GLY GLU ALA TPO VAL PTR ALA 0.416667 0.666667
96 GLU GLU PHE GLY ARG ALA PHE SER PHE 0.414474 0.730159
97 GLY ARG PHE ALA ALA ALA ILE ALA LYS 0.413793 0.813559
98 GLY ALA ASP ILE PHE TYR LEU ASP GLY ALA 0.413793 0.745763
99 PHE TYR ARG TYR GLY PHE VAL ALA ASN PHE 0.413333 0.806452
100 GLY TYR GLU ASN PRO THR TYR LYS PHE PHE 0.413174 0.608108
101 ILE ARG LYS ILE LEU PHE LEU ASP GLY ILE 0.4125 0.833333
102 ARG ILE PRO SER TYR ARG TYR ARG TYR 0.4125 0.693333
103 GLY ALA ARG 0.412281 0.714286
104 ACE GLU ASN LEU TYR PHE GLN SER GLY THR 0.412162 0.737705
105 HIS LYS ILE LEU HIS ARG LEU LEU GLN GLU 0.411043 0.753846
106 GLU ALA GLN THR ARG LEU 0.410072 0.79661
107 ARG PRO MET THR TYR LYS GLY ALA LEU 0.409091 0.733333
108 ALA PRO ALA LEU ARG VAL VAL LYS 0.407692 0.789474
109 ALA LEU TYR ASN THR ALA ALA ALA LEU 0.407143 0.7
110 GLY ARG PRO ARG THR THR SER PHE ALA GLU 0.404762 0.694444
111 PHE LEU ALA TYR LYS 0.402878 0.745763
112 ARG ARG LEU LEU ARG GLY HIS ASN GLN TYR 0.402439 0.833333
113 SER LEU TYR ASN VAL VAL ALA THR LEU 0.401361 0.721311
114 MET ABA LEU ARG MET THR ALA VAL MET 0.401361 0.734375
115 LEU LEU TYR GLY PHE VAL ASN TYR VAL 0.401316 0.725806
116 LEU ALA ILE TYR SER 0.4 0.711864
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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