Receptor
PDB id Resolution Class Description Source Keywords
4LKM 2 Å EC: 2.7.1.- 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: 2.7.1.- 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 15 families.
1 1Q4K Kd = 280 nM MET GLN SER TPO PRO LEU n/a n/a
2 3HIK Kd = 0.445 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 Kd = 3 nM 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 = 1.8 uM 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 12 families.
1 1Q4K Kd = 280 nM MET GLN SER TPO PRO LEU n/a n/a
2 3HIK Kd = 0.445 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 Kd = 3 nM 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 = 1.8 uM 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 9 families.
1 1Q4K Kd = 280 nM MET GLN SER TPO PRO LEU n/a n/a
2 3HIK Kd = 0.445 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 Kd = 3 nM 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 = 1.8 uM 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 (2D)
Ligand no: 1; Ligand: 5PV ACE PRO LEU HIS SER TPO MET NH2 LYT; Similar ligands found: 19
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 ARG SER HIS SEP SER PRO ALA SER LEU GLN 0.43299 0.875
13 SER HIS SEP SER PRO ALA SER LEU GLN 0.430108 0.921053
14 ACE PRO LEU 56A SER TPO NH2 0.428571 0.911392
15 SER ARG ASP HIS SER ARG THR PRO MET 0.428571 0.839506
16 ACE PRO LEU 2SO SER TPO NH2 0.423913 0.924051
17 ARG ALA HIS SEP SER PRO ALA SER LEU GLN 0.413408 0.896104
18 SER HIS SEP SER PRO ALA SER LEU 0.411111 0.907895
19 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: 32
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 ARG ALA HIS SEP SER PRO ALA SER LEU GLN 0.476821 0.907895
15 SER HIS SEP SER PRO ALA SER LEU GLN 0.45679 0.907895
16 SER ARG ASP HIS SER ARG THR PRO MET 0.454545 0.82716
17 SER HIS SEP SER PRO ALA SER LEU 0.454545 0.92
18 ARG SER HIS SEP SER PRO ALA SER LEU GLN 0.433526 0.8625
19 MET LEU LEU SER VAL PRO LEU LEU LEU GLY 0.428571 0.776316
20 ACE MET GLN SER SEP PRO LEU NH2 0.421769 0.894737
21 TYR TYR SER ILE ILE PRO HIS SER ILE 0.417722 0.756098
22 MET GLN SER TPO PRO LEU 0.417219 0.894737
23 LYS PRO HIS SER ASP 0.416667 0.753247
24 LEU LEU CYS SER TPO PRO ASN GLY LEU 0.410596 0.868421
25 PRO MET GLN SER TPO PRO LEU 0.410256 0.921053
26 TYR TYR SER ILE ALA PRO HIS SER ILE 0.407407 0.777778
27 ACE ALA PRO GLN VAL STA VAL MET HIS PRO 0.403614 0.857143
28 ABA SER LEU TRP ASN GLY PRO HIS LEU 0.403509 0.765432
29 PHE ASN GLU LEU SER HIS LEU 0.402985 0.662338
30 HIS PRO HIS LEU SER 13E ALA HIS 0.402439 0.75641
31 ARG LEU TYR HIS SEP LEU PRO ALA 0.401163 0.831325
32 HIS SER LEU PHE HIS PUK THR PRO 0.4 0.797468
Similar Ligands (3D)
Ligand no: 1; Ligand: 5PV ACE PRO LEU HIS SER TPO MET NH2 LYT; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 2; Ligand: ACE PRO LEU HIS SER TPO MET NH2; Similar ligands found: 0
No: Ligand Similarity coefficient
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: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4o6w.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
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