Receptor
PDB id Resolution Class Description Source Keywords
4EQ0 1.7 Å EC: 3.4.23.16 CRYSTAL STRUCTURE OF INACTIVE SINGLE CHAIN VARIANT OF HIV-1 IN COMPLEX WITH THE SUBSTRATE P2-NC HIV-1 M:B_ARV2/SF2 HIV-1 PROTEASE SPECIFICITY DESIGN DRUG DESIGN PROTEASE INAIDS ASPARTYL PROTEASE HYDROLASE HYDROLASE-HYDROLASE SUBCOMPLEX
Ref.: STRUCTURAL, KINETIC, AND THERMODYNAMIC STUDIES OF SPECIFICITY DESIGNED HIV-1 PROTEASE. PROTEIN SCI. V. 21 1029 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACT A:205;
Invalid;
none;
submit data
59.044 C2 H3 O2 CC(=O...
ALA THR ILE MET MET GLN ARG GLY P:2;
Valid;
none;
submit data
719.95 n/a S(CCC...
BME A:201;
Invalid;
none;
submit data
78.133 C2 H6 O S C(CS)...
EDO A:202;
A:204;
A:206;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
GOL A:203;
A:207;
A:208;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
PO4 A:209;
Invalid;
none;
submit data
94.971 O4 P [O-]P...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3KA2 1.4 Å EC: 3.4.23.16 CRYSTAL STRUCTURE OF CHEMICALLY SYNTHESIZED 203 AMINO ACID ' DIMER' [L-ALA;GLY51']HIV-1 PROTEASE MOLECULE COMPLEXED WITHR EDUCED ISOSTERE INHIBITOR AT 1.4 A RESOLUTION - BETA-BARREL HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: PROTEIN CONFORMATIONAL DYNAMICS IN THE MECHANISM OF PROTEASE CATALYSIS. PROC.NATL.ACAD.SCI.USA V. 108 20982 2011
Members (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 27 families.
1 4EQ0 - ALA THR ILE MET MET GLN ARG GLY n/a n/a
2 4EP3 - LYS ALA ARG VAL LEU ALA GLU ALA MET n/a n/a
3 3KA2 Kd = 0.24 uM 2NC C35 H68 N11 O8 CCCC[C@@H]....
4 3HLO Kd = 0.61 uM 2NC C35 H68 N11 O8 CCCC[C@@H]....
5 4EPJ - ALA THR ILE MET MET GLN ARG GLY n/a n/a
6 1HVC - A79 C44 H58 N8 O6 CC(C)[C@@H....
7 2WHH - PPN C9 H10 N2 O4 c1cc(ccc1C....
8 3N3I - ROC C38 H50 N6 O5 CC(C)(C)NC....
9 4EQJ Kd = 2.52 uM ALA GLU THR PHE TYR VAL ASP GLY n/a n/a
70% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 families.
1 2O40 - 2NC C35 H68 N11 O8 CCCC[C@@H]....
2 3NXN - KVS C36 H68 N10 O10 [H]/N=C(N)....
3 3IAW Kd = 1.57 uM 2NC C35 H68 N11 O8 CCCC[C@@H]....
4 3NXE - 2NC C35 H68 N11 O8 CCCC[C@@H]....
5 3FSM Kd = 100 nM 2NC C35 H68 N11 O8 CCCC[C@@H]....
6 4EP2 Kd = 4.43 uM ALA GLU THR PHE TYR VAL ASP GLY n/a n/a
7 4EQ0 - ALA THR ILE MET MET GLN ARG GLY n/a n/a
8 4EP3 - LYS ALA ARG VAL LEU ALA GLU ALA MET n/a n/a
9 3KA2 Kd = 0.24 uM 2NC C35 H68 N11 O8 CCCC[C@@H]....
10 3HLO Kd = 0.61 uM 2NC C35 H68 N11 O8 CCCC[C@@H]....
11 4EPJ - ALA THR ILE MET MET GLN ARG GLY n/a n/a
12 1HVC - A79 C44 H58 N8 O6 CC(C)[C@@H....
13 2WHH - PPN C9 H10 N2 O4 c1cc(ccc1C....
14 3N3I - ROC C38 H50 N6 O5 CC(C)(C)NC....
15 4EQJ Kd = 2.52 uM ALA GLU THR PHE TYR VAL ASP GLY n/a n/a
16 3DOX - SER GLN ASN TYR n/a n/a
17 4Q5M - ROC C38 H50 N6 O5 CC(C)(C)NC....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 families.
1 2O40 - 2NC C35 H68 N11 O8 CCCC[C@@H]....
2 3NXN - KVS C36 H68 N10 O10 [H]/N=C(N)....
3 4EQ0 - ALA THR ILE MET MET GLN ARG GLY n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: ALA THR ILE MET MET GLN ARG GLY; Similar ligands found: 27
No: Ligand ECFP6 Tc MDL keys Tc
1 ALA THR ILE MET MET GLN ARG GLY 1 1
2 ALA LYS ALA ILE ALA 0.54023 0.809524
3 ALA GLU ALA ALA GLN ALA 0.511628 0.780488
4 GLU ALA THR GLN LEU MET ASN 0.490385 0.808511
5 PRO ALA THR ILE MET MET GLN ARG GLY ASN 0.481132 0.709091
6 THR ILE MET MET GLN ARG GLY 0.471698 0.696429
7 ALA LYS ALA SER GLN ALA ALA 0.458333 0.6875
8 MET GLU ASP TPO GLN ALA ILE ASP 0.448276 0.722222
9 ALA LEU SER ARG 0.443038 0.630435
10 ASP GLN ILE ILE 0.4375 0.707317
11 ALA ILE PHE GLN SER SER MET THR LYS 0.434426 0.709091
12 ALA ALA SER ALA SER ALA 0.432099 0.617021
13 GLN ILE IL0 ILE GLU ILE ALA 0.431373 0.717391
14 ARG ILE MET GLU NH2 0.431373 0.795918
15 ALA SER ASN GLU ASN ILE GLU THR MET 0.431193 0.764706
16 ALA ARG THR LYS GLN THR ALA ARG LYS SER 0.430108 0.653061
17 TYR ASP GLN ILE ILE ILE 0.428571 0.761905
18 ACE ARG LYS VAL ARG MET 5XU 0.425532 0.770833
19 ILE MET ILE SER PHE 0.419048 0.755102
20 ALA LEU LYS ILE ASP ASN MET ASP 0.417391 0.78
21 ALA LEU SER ARG GLN 0.414634 0.630435
22 ALA ILE GLU THR ASA 0.40625 0.702128
23 ILE GLU ILE 0.404762 0.804878
24 ALA ALA LEU THR ARG ALA 0.403846 0.611111
25 SER LEU LEU MET TRP ILE THR GLN VAL 0.402985 0.65
26 SER LEU LEU MET TRP ILE THR GLN ALA 0.401515 0.639344
27 LYS ILE ALA ALA 0.4 0.785714
Similar Ligands (3D)
Ligand no: 1; Ligand: ALA THR ILE MET MET GLN ARG GLY; 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 : 3KA2; Ligand: 2NC; Similar sites found with APoc: 3
This union binding pocket(no: 1) in the query (biounit: 3ka2.bio1) has 68 residues
No: Leader PDB Ligand Sequence Similarity
1 3WSJ MK1 17.2414
2 3WSJ MK1 17.2414
3 1BAI 0Q4 38.7097
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