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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 (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 39 families.
1 2G99 - ALA ARG THR MLY GLN THR ALA ARG MLY SER n/a n/a
2 6DAI - G2V C15 H17 N3 CN1CCc2c1c....
3 2CNX - ALA ARG THR MLY GLN n/a n/a
4 3UVM Kd = 0.03 uM GLY ALA ALA ARG ALA GLU VAL TYR LEU ARG n/a n/a
5 2H6K Kd = 8.7 uM ALA ARG THR MLZ GLN THR ALA ARG LYS n/a n/a
6 2H6Q Kd = 7.8 uM ALA ARG THR M3L GLN THR ALA ARG LYS n/a n/a
7 4Y7R Kd = 9.3 uM GLU GLU ILE ASP VAL VAL SER VAL n/a n/a
8 6DAK Ki = 7.21 uM G1Y C20 H19 N3 O c1ccc(cc1)....
9 5SXM Kd = 3 nM ACE ALA ARG THR GLU VAL TYR NH2 n/a n/a
10 3PSL - ACE ALA ARG THR LYS GLN n/a n/a
11 6D9X Ki = 323 uM FZM C12 H12 N2 c1ccc(cc1)....
12 6DAS Ki = 8.37 nM G2D C24 H25 N3 O2 Cc1ccc(cc1....
13 6DAR Ki = 0.219 uM G2J C25 H27 N3 O2 COc1cccc(c....
14 5VFC ic50 = 0.9 nM 9BA C28 H44 N8 O5 [H]/N=C(NC....
15 2H13 Kd = 4.5 uM ALA ARG THR MLY GLN THR ALA ARG LYS SER n/a n/a
16 2H6N Kd = 1.02 uM ALA ARG THR MLY GLN THR ALA ARG LYS n/a n/a
70% Homology Family (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 28 families.
1 2G99 - ALA ARG THR MLY GLN THR ALA ARG MLY SER n/a n/a
2 6DAI - G2V C15 H17 N3 CN1CCc2c1c....
3 2CNX - ALA ARG THR MLY GLN n/a n/a
4 3UVM Kd = 0.03 uM GLY ALA ALA ARG ALA GLU VAL TYR LEU ARG n/a n/a
5 2H6K Kd = 8.7 uM ALA ARG THR MLZ GLN THR ALA ARG LYS n/a n/a
6 2H6Q Kd = 7.8 uM ALA ARG THR M3L GLN THR ALA ARG LYS n/a n/a
7 4Y7R Kd = 9.3 uM GLU GLU ILE ASP VAL VAL SER VAL n/a n/a
8 6DAK Ki = 7.21 uM G1Y C20 H19 N3 O c1ccc(cc1)....
9 5SXM Kd = 3 nM ACE ALA ARG THR GLU VAL TYR NH2 n/a n/a
10 3PSL - ACE ALA ARG THR LYS GLN n/a n/a
11 6D9X Ki = 323 uM FZM C12 H12 N2 c1ccc(cc1)....
12 6DAS Ki = 8.37 nM G2D C24 H25 N3 O2 Cc1ccc(cc1....
13 6DAR Ki = 0.219 uM G2J C25 H27 N3 O2 COc1cccc(c....
14 5VFC ic50 = 0.9 nM 9BA C28 H44 N8 O5 [H]/N=C(NC....
15 2H13 Kd = 4.5 uM ALA ARG THR MLY GLN THR ALA ARG LYS SER n/a n/a
16 2H6N Kd = 1.02 uM ALA ARG THR MLY GLN THR ALA ARG LYS n/a n/a
50% Homology Family (16)
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 6DAI - G2V C15 H17 N3 CN1CCc2c1c....
3 2CNX - ALA ARG THR MLY GLN n/a n/a
4 3UVM Kd = 0.03 uM GLY ALA ALA ARG ALA GLU VAL TYR LEU ARG n/a n/a
5 2H6K Kd = 8.7 uM ALA ARG THR MLZ GLN THR ALA ARG LYS n/a n/a
6 2H6Q Kd = 7.8 uM ALA ARG THR M3L GLN THR ALA ARG LYS n/a n/a
7 4Y7R Kd = 9.3 uM GLU GLU ILE ASP VAL VAL SER VAL n/a n/a
8 6DAK Ki = 7.21 uM G1Y C20 H19 N3 O c1ccc(cc1)....
9 5SXM Kd = 3 nM ACE ALA ARG THR GLU VAL TYR NH2 n/a n/a
10 3PSL - ACE ALA ARG THR LYS GLN n/a n/a
11 6D9X Ki = 323 uM FZM C12 H12 N2 c1ccc(cc1)....
12 6DAS Ki = 8.37 nM G2D C24 H25 N3 O2 Cc1ccc(cc1....
13 6DAR Ki = 0.219 uM G2J C25 H27 N3 O2 COc1cccc(c....
14 5VFC ic50 = 0.9 nM 9BA C28 H44 N8 O5 [H]/N=C(NC....
15 2H13 Kd = 4.5 uM ALA ARG THR MLY GLN THR ALA ARG LYS SER n/a n/a
16 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: 90
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 0.769231 0.966667
3 ALA ARG THR MLY GLN THR ALA 0.769231 0.966667
4 ALA ARG THR MLY GLN THR ALA ARG LYS 0.76087 0.983051
5 ALA ARG THR MLY GLN THR ALA ARG MLY SER 0.744444 0.983051
6 ARG ARG ARG GLU THR GLN VAL 0.663043 0.833333
7 ALA ARG THR MLY GLN THR ALA ARG TYR 0.66055 0.893939
8 ALA ARG THR M3L GLN THR ALA ARG 0.65 0.951613
9 ALA ARG THR M3L GLN THR ALA 0.606061 0.935484
10 ALA ARG THR M3L GLN THR ALA 2MR LYS 0.606061 0.935484
11 ALA ARG THR ALY GLN THR ALA 0.606061 0.85
12 ALA ARG THR LYS GLN THR ALA ARG 0.604167 0.830508
13 ALA ARG THR MLZ GLN THR ALA ARG LYS TYR 0.60396 0.915254
14 ALA ARG THR M3L GLN THR ALA ARG LYS SER 0.6 0.935484
15 ALA ARG THR M3L GLN THR ALA ARG LYS 0.6 0.935484
16 ALA 2MR THR MLY GLN THR ALA ALA 0.59596 0.966667
17 THR ARG ARG GLU THR GLN LEU 0.58 0.85
18 ALA ARG THR MLY GLN THR ALA ARG LYS SER 0.578947 0.783333
19 ALA ARG MLY SER THR GLY GLY ALY 0.570175 0.951613
20 ALA ARG THR M3L GLN THR ALA ALA LYS ALA 0.567568 0.951613
21 ALA ARG THR LYS GLN THR ALA ARG LYS 0.566038 0.816667
22 ALA ARG 9AT 0.560976 0.779661
23 ALA ARG THR MLZ GLN THR ALA ARG LYS 0.559633 0.9
24 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.556604 0.85
25 GLU ALA GLN THR ARG LEU 0.542056 0.847458
26 PHE ALA GLY LEU ARG GLN ALA VAL THR GLN 0.541284 0.833333
27 ALA ARG THR 4WQ GLN THR ALA ARG LYS SER 0.540816 0.852459
28 SAC ARG GLY THR GLN THR GLU 0.522936 0.790323
29 ACE GLU ALA GLN THR ARG LEU 0.518519 0.864407
30 ALA ARG THR ALA ALA THR ALA ARG LYS SER 0.494949 0.766667
31 ALA ARG THR GLU LEU TYR ARG SER LEU 0.491803 0.761194
32 ALA DA2 THR M3L GLN THR ALA ARG ALA 0.487603 0.935484
33 LEU GLY GLY ALA LYS GLN ARG GLY ASP VAL 0.486486 0.783333
34 ALA ARG 0.481481 0.677966
35 ALA PRO ALA LEU ARG VAL VAL LYS 0.471154 0.779661
36 ALA ALA LEU THR ARG ALA 0.471154 0.813559
37 ALA THR VAL ARG THR TYR SER CYS 0.466102 0.705882
38 PRO ALA THR ILE MET MET GLN ARG GLY ASN 0.464286 0.83871
39 LYS GLN THR SER VAL 0.462366 0.672131
40 ARG HIS ARG MLY VAL LEU ARG ASP ASN 0.461538 0.811594
41 ALA ARG ALA ALA ALA ALA ALA ALA ALA 0.461538 0.711864
42 ALA ARG M3L SER THR GLY GLY ALY 0.459016 0.921875
43 LYS ALA THR LYS MLY 0.456522 0.881356
44 ALA GLN PHE SER ALA SER ALA SER ARG 0.45614 0.734375
45 ALA ARG LYS LEU ASP 0.455446 0.813559
46 THR ILE MET MET GLN ARG GLY 0.455357 0.854839
47 ALA ARG MLZ SER THR GLY GLY ALY 0.455285 0.887097
48 ACE GLN THR ALA ARG PRK SER THR 0.452991 0.806452
49 ALA ARG THR M3L GLN THR ALA DA2 LYS 0.451128 0.935484
50 ARG HIS ARG MLY VAL LEU ARG ASP TYR 0.449275 0.780822
51 GLN ARG ALA THR LYS MET NH2 0.444444 0.883333
52 LYS ARG ARG LYS SEP VAL 0.443396 0.716418
53 ILE GLN GLN SER ILE GLU ARG ILE 0.442478 0.803279
54 LYS ARG LYS 0.44086 0.711864
55 ALA ARG M3L SER 0.44 0.857143
56 ALA GLN THR ALA ARG ALY SER THR 0.436975 0.836066
57 ASN SER THR LEU GLN 0.435644 0.66129
58 GLN THR ALA ARG M3L SER 0.432203 0.920635
59 SER SER ARG LYS GLU TYR TYR ALA 0.431034 0.701493
60 ALA MET ALA PRO ARG THR LEU LEU LEU 0.426357 0.84058
61 ACE GLN THR ALA ARG KCR SER THR 0.42623 0.819672
62 ARG ARG ALA THR LYS MET NH2 0.426087 0.852459
63 ACE GLN THR ALA ARG BTK SER THR 0.423729 0.836066
64 VAL ALA ARG SER 0.42268 0.75
65 ALA ASN SER ARG TRP GLN ASP THR ARG LEU 0.422535 0.69863
66 ALA THR ARG ASN PHE SER GLY 0.421488 0.712121
67 ACE ALA ARG THR GLU VAL TYR NH2 0.421488 0.753846
68 ACE ALA ARG THR LYS GLN 0.420561 0.813559
69 ALA GLU THR PHE 0.42 0.612903
70 MET ABA LEU ARG MET THR ALA VAL MET 0.419355 0.868852
71 GLN THR ALA ARG M3L SER THR GLY 0.419355 0.920635
72 ILE LYS ARG SER MLZ LYS ASN SER LEU ALA 0.419048 0.866667
73 LYS ARG HIS ARG MLY VAL LEU ARG ASP ASN 0.417582 0.79661
74 ACE CSO ARG ALA THR LYS MET LEU 0.416 0.835821
75 ALA ILE ARG SER 0.415842 0.721311
76 GLU THR VAL ARG PHE GLN SER ASP 0.415385 0.777778
77 GLU ARG GLY MET THR 0.414414 0.819672
78 ALA ASN SER ARG TRP GLN THR SER ILE ILE 0.412587 0.662162
79 ILE LYS ARG SER LYS LYS ASN SER LEU ALA 0.411765 0.766667
80 ARG GLU ARG SER PRO THR ARG 0.410714 0.724638
81 SER ASP TYR GLN ARG LEU 0.410256 0.738462
82 ALA PHE ARG ILE PRO LEU THR ARG 0.410072 0.75
83 MET CYS LEU ARG MET THR ALA VAL MET 0.409449 0.868852
84 GLY HIS LYS ILE LEU HIS ARG LEU LEU GLN 0.409091 0.661972
85 ASN ARG LEU MET LEU THR GLY 0.408696 0.854839
86 ALA ARG MLZ SER ALA PRO ALA THR 0.40458 0.814286
87 ALA ARG LYS ILE ASP ASN LEU ASP 0.403226 0.777778
88 ALA ASN SER ARG VAL GLN ASP SER ILE ILE 0.403226 0.765625
89 ALA ARG LYS SEP THR GLY GLY LYS 0.401575 0.735294
90 MET CYS LEU ARG NLE THR ALA VAL MET 0.4 0.854839
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5VFC; Ligand: 9BA; Similar sites found with APoc: 55
This union binding pocket(no: 1) in the query (biounit: 5vfc.bio1) has 34 residues
No: Leader PDB Ligand Sequence Similarity
1 5ACM MBT None
2 3S6X SIA GAL BGC 1.28617
3 4UMJ BFQ 1.35135
4 5G3R 89A 1.60772
5 4RT1 C2E 1.78571
6 4WGF HX2 1.95122
7 5LUN ARG 2.2508
8 1C1X HFA 2.2508
9 2J83 BAT 2.29008
10 4Q0A 4OA 2.31788
11 5M3Z PY6 2.57235
12 4ZTD ALA GLY ALA GLY ALA 2.7668
13 2YBP 2HG 2.89389
14 4D06 NAR 3.18021
15 1RZM E4P 3.53698
16 1FUR MLT 3.53698
17 5KJW 53C 3.53698
18 5VJN ADE 3.74332
19 1OFU GDP 3.75
20 4IY7 KOU 3.85852
21 3G5N PB2 3.85852
22 4K79 GAL A2G 4.09091
23 3BP1 GUN 4.13793
24 6EWZ APC 4.21941
25 3THR C2F 4.77816
26 4K55 H6P 4.83871
27 1EXF GLY 4.95868
28 2PIE GLU LEU LYS TPO GLU ARG TYR 5.07246
29 3M89 GSP 5.14469
30 5ARK UMP 5.22388
31 6G47 SIA 5.26316
32 3K3G MMU 5.46624
33 3AIH BMA MAN MAN 5.64516
34 1FQK ALF 5.78778
35 1FQJ ALF 5.78778
36 5O2J 2PO 6.22711
37 5MVR ADP 6.79012
38 4GNC ASO 7.02341
39 3E3U NVC 7.1066
40 4O4Z N2O 7.14286
41 3OUM TOF 7.32759
42 2VDF OCT 7.50988
43 6EOM ALA LYS 8.03859
44 5JVB 2PO 9.28571
45 4EZD SEY 9.32476
46 3FSY SCA 9.33735
47 6MJ7 ARG 10.9091
48 1LSH PLD 13.8264
49 5TEF GTG 15.4341
50 5HWV MBN 17.6923
51 5WUK 73K 21.2219
52 5U6D 7XG 21.2219
53 1Z0N BCD 26.0417
54 5MWJ EBU 33.119
55 4J8B LEU LYS THR LYS LEU LEU 41.8006
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