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Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:404;
A:407;
A:408;
A:405;
A:406;
A:409;
A:403;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
SO4 A:402;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
9BA A:401;
Valid;
none;
ic50 = 0.9 nM
572.7 C28 H44 N8 O5 [H]/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 (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: 9BA; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 9BA 1 1
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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