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Receptor
PDB id Resolution Class Description Source Keywords
4LKM 2 Å EC: 2.7.11.21 CRYSTAL STRUCTURE OF PLK1 POLO-BOX DOMAIN IN COMPLEX WITH PL HOMO SAPIENS POLO-BOX DOMAIN TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: EXPLORING THE BINDING NATURE OF PYRROLIDINE POCKET-INTERACTIONS IN THE POLO-BOX DOMAIN OF POLO-LIKE KI PLOS ONE V. 8 80043 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:701;
C:701;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
5PV ACE PRO LEU HIS SER TPO MET NH2 LYT B:101;
Valid;
none;
ic50 = 0.46 uM
1042.23 n/a S(CCC...
ACE PRO LEU HIS SER TPO MET NH2 D:0;
Valid;
none;
submit data
804.84 n/a S(CCC...
GOL B:103;
D:301;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4O6W 1.45 Å EC: 2.7.11.21 PEPTIDE-BASED INHIBITORS OF PLK1 POLO-BOX DOMAIN HOMO SAPIENS POLO BOX DOMAIN PHOSPHO-PEPTIDE BINDING PHOSPHOPEPTIDE TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: MONO-ANIONIC PHOSPHOPEPTIDES PRODUCED BY UNEXPECTED HISTIDINE ALKYLATION EXHIBIT HIGH PLK1 POLO-BOX DOMAIN-BINDING AFFINITIES AND ENHANCED ANTIPROLIFER EFFECTS IN HELA CELLS. BIOPOLYMERS V. 102 444 2014
Members (25)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1Q4K Kd = 280 nM MET GLN SER TPO PRO LEU n/a n/a
2 3HIK Kd = 0.262 uM ACE PRO LEU HIS SER TPO n/a n/a
3 4X9V ic50 = 0.014 uM 4KY LEU 56A SER TPO NH2 n/a n/a
4 3FVH Kd = 0.447 uM ACE LEU HIS SER TPO ALA NH2 n/a n/a
5 5DNJ - 707 56A SER TPO NH2 n/a n/a
6 1UMW Kd = 280 nM PRO MET GLN SER TPO PRO LEU n/a n/a
7 4RCP ic50 = 4.42 uM ACE 56A SER TPO NH2 n/a n/a
8 4LKL ic50 = 0.82 uM ACE PRO LEU HIS SER TPO MET NH2 ADM n/a n/a
9 4LKM ic50 = 0.46 uM 5PV ACE PRO LEU HIS SER TPO MET NH2 LYT n/a n/a
10 3C5L - PRO PRO HIS SER TPO n/a n/a
11 4E67 - HCI PRO LEU HIS SER TPO ALA NH2 n/a n/a
12 3P2Z - ACE PRO LEU HIS SER TPO ALA NH2 n/a n/a
13 4WHK - YAC 56A SER TPO NH2 n/a n/a
14 4X9W ic50 = 0.14 uM LEU 3ZH SER TPO NH2 n/a n/a
15 4WHH ic50 = 0.04 uM QAC 56A SER TPO NH2 n/a n/a
16 4DFW ic50 = 0.014 uM ACE 0LF LEU HIS SER TPO NH2 n/a n/a
17 3RQ7 ic50 = 0.017 uM ACE PRO LEU 56A SER TPO NH2 n/a n/a
18 5DMS Kd = 29.58 uM PHE SER GLN HIS LYS THR SER TPO ILE n/a n/a
19 3P36 Kd = 2.14 uM ACE ASP PRO PRO LEU HIS SER TPO ALA NH2 n/a n/a
20 4X9R ic50 = 0.015 uM 4L0 LEU 56A SER TPO NH2 n/a n/a
21 3P35 - ACE MET GLN SER SEP PRO LEU NH2 n/a n/a
22 4O6W ic50 = 0.001 uM ACE PRO LEU 2SO SER TPO NH2 n/a n/a
23 4HY2 - 1C3 LEU HIS SER TPO MET NH2 n/a n/a
24 6AX4 - N7P LEU 56A SER TPO AML n/a n/a
25 3BZI Kd = 1.05 mM LEU LEU CYS SER TPO PRO ASN GLY LEU n/a n/a
70% Homology Family (26)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1Q4K Kd = 280 nM MET GLN SER TPO PRO LEU n/a n/a
2 3HIK Kd = 0.262 uM ACE PRO LEU HIS SER TPO n/a n/a
3 4X9V ic50 = 0.014 uM 4KY LEU 56A SER TPO NH2 n/a n/a
4 3FVH Kd = 0.447 uM ACE LEU HIS SER TPO ALA NH2 n/a n/a
5 5DNJ - 707 56A SER TPO NH2 n/a n/a
6 1UMW Kd = 280 nM PRO MET GLN SER TPO PRO LEU n/a n/a
7 4RCP ic50 = 4.42 uM ACE 56A SER TPO NH2 n/a n/a
8 4LKL ic50 = 0.82 uM ACE PRO LEU HIS SER TPO MET NH2 ADM n/a n/a
9 4LKM ic50 = 0.46 uM 5PV ACE PRO LEU HIS SER TPO MET NH2 LYT n/a n/a
10 3C5L - PRO PRO HIS SER TPO n/a n/a
11 4E67 - HCI PRO LEU HIS SER TPO ALA NH2 n/a n/a
12 3P2Z - ACE PRO LEU HIS SER TPO ALA NH2 n/a n/a
13 4WHK - YAC 56A SER TPO NH2 n/a n/a
14 4X9W ic50 = 0.14 uM LEU 3ZH SER TPO NH2 n/a n/a
15 4WHH ic50 = 0.04 uM QAC 56A SER TPO NH2 n/a n/a
16 4DFW ic50 = 0.014 uM ACE 0LF LEU HIS SER TPO NH2 n/a n/a
17 3RQ7 ic50 = 0.017 uM ACE PRO LEU 56A SER TPO NH2 n/a n/a
18 5DMS Kd = 29.58 uM PHE SER GLN HIS LYS THR SER TPO ILE n/a n/a
19 3P36 Kd = 2.14 uM ACE ASP PRO PRO LEU HIS SER TPO ALA NH2 n/a n/a
20 4X9R ic50 = 0.015 uM 4L0 LEU 56A SER TPO NH2 n/a n/a
21 3P35 - ACE MET GLN SER SEP PRO LEU NH2 n/a n/a
22 4O6W ic50 = 0.001 uM ACE PRO LEU 2SO SER TPO NH2 n/a n/a
23 4HY2 - 1C3 LEU HIS SER TPO MET NH2 n/a n/a
24 6AX4 - N7P LEU 56A SER TPO AML n/a n/a
25 3BZI Kd = 1.05 mM LEU LEU CYS SER TPO PRO ASN GLY LEU n/a n/a
26 3P34 - ACE MET GLN SER TPO PRO LEU NH2 n/a n/a
50% Homology Family (26)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1Q4K Kd = 280 nM MET GLN SER TPO PRO LEU n/a n/a
2 3HIK Kd = 0.262 uM ACE PRO LEU HIS SER TPO n/a n/a
3 4X9V ic50 = 0.014 uM 4KY LEU 56A SER TPO NH2 n/a n/a
4 3FVH Kd = 0.447 uM ACE LEU HIS SER TPO ALA NH2 n/a n/a
5 5DNJ - 707 56A SER TPO NH2 n/a n/a
6 1UMW Kd = 280 nM PRO MET GLN SER TPO PRO LEU n/a n/a
7 4RCP ic50 = 4.42 uM ACE 56A SER TPO NH2 n/a n/a
8 4LKL ic50 = 0.82 uM ACE PRO LEU HIS SER TPO MET NH2 ADM n/a n/a
9 4LKM ic50 = 0.46 uM 5PV ACE PRO LEU HIS SER TPO MET NH2 LYT n/a n/a
10 3C5L - PRO PRO HIS SER TPO n/a n/a
11 4E67 - HCI PRO LEU HIS SER TPO ALA NH2 n/a n/a
12 3P2Z - ACE PRO LEU HIS SER TPO ALA NH2 n/a n/a
13 4WHK - YAC 56A SER TPO NH2 n/a n/a
14 4X9W ic50 = 0.14 uM LEU 3ZH SER TPO NH2 n/a n/a
15 4WHH ic50 = 0.04 uM QAC 56A SER TPO NH2 n/a n/a
16 4DFW ic50 = 0.014 uM ACE 0LF LEU HIS SER TPO NH2 n/a n/a
17 3RQ7 ic50 = 0.017 uM ACE PRO LEU 56A SER TPO NH2 n/a n/a
18 5DMS Kd = 29.58 uM PHE SER GLN HIS LYS THR SER TPO ILE n/a n/a
19 3P36 Kd = 2.14 uM ACE ASP PRO PRO LEU HIS SER TPO ALA NH2 n/a n/a
20 4X9R ic50 = 0.015 uM 4L0 LEU 56A SER TPO NH2 n/a n/a
21 3P35 - ACE MET GLN SER SEP PRO LEU NH2 n/a n/a
22 4O6W ic50 = 0.001 uM ACE PRO LEU 2SO SER TPO NH2 n/a n/a
23 4HY2 - 1C3 LEU HIS SER TPO MET NH2 n/a n/a
24 6AX4 - N7P LEU 56A SER TPO AML n/a n/a
25 3BZI Kd = 1.05 mM LEU LEU CYS SER TPO PRO ASN GLY LEU n/a n/a
26 3P34 - ACE MET GLN SER TPO PRO LEU NH2 n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5PV ACE PRO LEU HIS SER TPO MET NH2 LYT; Similar ligands found: 17
No: Ligand ECFP6 Tc MDL keys Tc
1 5PV ACE PRO LEU HIS SER TPO MET NH2 LYT 1 1
2 ACE PRO LEU HIS SER TPO MET NH2 0.722222 0.961039
3 ACE PRO LEU HIS SER TPO MET NH2 ADM 0.685897 0.95
4 HCI PRO LEU HIS SER TPO ALA NH2 0.61875 0.935065
5 ACE PRO LEU HIS SER TPO ALA NH2 0.61745 0.922078
6 ACE ASP PRO PRO LEU HIS SER TPO ALA NH2 0.561728 0.921053
7 ACE PRO LEU HIS SER TPO 0.556291 0.897436
8 1C3 LEU HIS SER TPO MET NH2 0.54386 0.926829
9 ACE LEU HIS SER TPO ALA NH2 0.496644 0.779221
10 ACE 0LF LEU HIS SER TPO NH2 0.449438 0.924051
11 PRO PRO HIS SER TPO 0.442424 0.87013
12 SER ARG ASP HIS SER ARG THR PRO MET 0.428571 0.839506
13 ACE PRO LEU 56A SER TPO NH2 0.428571 0.911392
14 ACE PRO LEU 2SO SER TPO NH2 0.423913 0.924051
15 ARG ALA HIS SEP SER PRO ALA SER LEU GLN 0.413408 0.896104
16 ACE MET GLN SER TPO PRO LEU NH2 0.411765 0.896104
17 ABA SER LEU TRP ASN GLY PRO HIS LEU 0.40625 0.8
Ligand no: 2; Ligand: ACE PRO LEU HIS SER TPO MET NH2; Similar ligands found: 29
No: Ligand ECFP6 Tc MDL keys Tc
1 ACE PRO LEU HIS SER TPO MET NH2 1 1
2 ACE PRO LEU HIS SER TPO ALA NH2 0.834783 0.96
3 ACE PRO LEU HIS SER TPO MET NH2 ADM 0.792308 0.91358
4 ACE PRO LEU HIS SER TPO 0.767241 0.934211
5 5PV ACE PRO LEU HIS SER TPO MET NH2 LYT 0.722222 0.961039
6 ACE ASP PRO PRO LEU HIS SER TPO ALA NH2 0.676692 0.933333
7 HCI PRO LEU HIS SER TPO ALA NH2 0.65942 0.897436
8 1C3 LEU HIS SER TPO MET NH2 0.636364 0.914634
9 ACE LEU HIS SER TPO ALA NH2 0.608333 0.813333
10 PRO PRO HIS SER TPO 0.540741 0.881579
11 ACE 0LF LEU HIS SER TPO NH2 0.540541 0.911392
12 ACE PRO LEU 2SO SER TPO NH2 0.526316 0.935897
13 ACE PRO LEU 56A SER TPO NH2 0.523179 0.923077
14 ACE MET GLN SER TPO PRO LEU NH2 0.489362 0.907895
15 ARG ALA HIS SEP SER PRO ALA SER LEU GLN 0.476821 0.907895
16 SER ARG ASP HIS SER ARG THR PRO MET 0.454545 0.82716
17 MET LEU LEU SER VAL PRO LEU LEU LEU GLY 0.428571 0.776316
18 ACE MET GLN SER SEP PRO LEU NH2 0.421769 0.894737
19 TYR TYR SER ILE ILE PRO HIS SER ILE 0.417722 0.756098
20 LYS TYR TYR SER ILE ILE PRO HIS SER ILE 0.417722 0.756098
21 MET GLN SER TPO PRO LEU 0.417219 0.894737
22 LYS PRO HIS SER ASP 0.416667 0.753247
23 LEU LEU CYS SER TPO PRO ASN GLY LEU 0.410596 0.868421
24 PRO MET GLN SER TPO PRO LEU 0.410256 0.921053
25 ACE ALA PRO GLN VAL STA VAL MET HIS PRO 0.409639 0.857143
26 TYR TYR SER ILE ALA PRO HIS SER ILE 0.407407 0.777778
27 ABA SER LEU TRP ASN GLY PRO HIS LEU 0.403509 0.765432
28 PHE ASN GLU LEU SER HIS LEU 0.402985 0.662338
29 ARG LEU TYR HIS SEP LEU PRO ALA 0.401163 0.831325
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4O6W; Ligand: ACE PRO LEU 2SO SER TPO NH2; Similar sites found with APoc: 33
This union binding pocket(no: 1) in the query (biounit: 4o6w.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 1PVC ILE SER GLU VAL 2.1097
3 5X80 SAL 2.5
4 1J78 OLA 2.53165
5 3HCH RSM 2.73973
6 6MVU K4V 2.95359
7 4DS0 A2G GAL NAG FUC 3.06748
8 1PWB GLC GLC 3.9548
9 5YXC CIT 4.16667
10 3SQP 3J8 4.21941
11 1XX4 BAM 4.21941
12 5WHT SIA 4.34783
13 5WHT SIA GAL 4.34783
14 5WHT SIA GAL GLC 4.34783
15 1TV5 N8E 4.64135
16 4LO6 SIA GAL 5.48523
17 4GNC ASO 5.48523
18 1KQR MNA 5.58659
19 3RV5 DXC 5.61798
20 1R6N 434 5.6872
21 4OWK NGA 5.7971
22 2P3I MNA 6.21118
23 6BR8 PGV 6.75105
24 1XZ3 ICF 6.89655
25 2BVE PH5 7.56302
26 1NF8 BOG 7.72947
27 5LX9 OLB 10.1266
28 1O9U ADZ 10.9705
29 5V4R MGT 12.3457
30 6GMN F4E 14.4231
31 4O4Z N2O 16.8831
32 3BGD PM6 20.2532
33 4LO2 GAL BGC 25.8503
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