Receptor
PDB id Resolution Class Description Source Keywords
6DTH 1.96 Å NON-ENZYME: BINDING CRYSTAL STRUCTURE OF HAEMOPHILUS INFLUENZAE OPPA COMPLEX WIT RPPGFSPFR HAEMOPHILUS INFLUENZAE (STRAIN 86-028NORGANISM_TAXID: 281310 SUBSTRATE-BINDING PROTEIN ABC TRANSPORTER PEPTIDE BINDING
Ref.: OLIGOPEPTIDE-BINDING PROTEIN FROM NONTYPEABLEHAEMOP INFLUENZAEHAS LIGAND-SPECIFIC SITES TO ACCOMMODATE AND HEME IN THE BINDING POCKET. J. BIOL. CHEM. V. 294 1070 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ARG PRO PRO GLY PHE B:1;
 Valid;
 Atoms found LESS than expected: % Diff = 0.024;
 submit data
558.684 n/a O=C(N...
SO4 A:601;
 Invalid;
 none;
 submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6DQU 1.65 Å NON-ENZYME: BINDING CRYSTAL STRUCTURE OF HAEMOPHILUS INFLUENZAE OPPA COMPLEX WIT HAEMOPHILUS INFLUENZAE (STRAIN 86-028NORGANISM_TAXID: 281310 SUBSTRATE-BINDING PROTEIN ABC TRANSPORTER PEPTIDE BINDING
Ref.: OLIGOPEPTIDE-BINDING PROTEIN FROM NONTYPEABLEHAEMOP INFLUENZAEHAS LIGAND-SPECIFIC SITES TO ACCOMMODATE AND HEME IN THE BINDING POCKET. J. BIOL. CHEM. V. 294 1070 2019
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 552 families.
1 6DQT - LEU GLY GLY n/a n/a
2 6DTG - TYR LEU GLY ALA ASN GLY n/a n/a
3 6DQR - MET GLY GLY n/a n/a
4 6DTH - ARG PRO PRO GLY PHE n/a n/a
5 6DQQ - ALA ALA ALA ALA n/a n/a
6 6DQU - GLY ILE ILE ASN THR LEU n/a n/a
7 6DTF - LYS LYS LYS n/a n/a
70% Homology Family (40)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 197 families.
1 1B5H Kd = 0.97 uM LYS DPP LYS n/a n/a
2 1B3G Kd = 200 nM LYS ILE LYS n/a n/a
3 1B40 Kd = 53 nM LYS PHE LYS n/a n/a
4 1JET Kd = 56 nM LYS ALA LYS n/a n/a
5 1B5I Kd = 90 nM LYS ASN LYS n/a n/a
6 1B5J Kd = 37 nM LYS GLN LYS n/a n/a
7 2OLB Kd = 2900 nM LYS LYS LYS n/a n/a
8 1B6H Kd = 0.015 uM LYS NVA LYS n/a n/a
9 1B7H Kd = 0.0095 uM LYS NLE LYS n/a n/a
10 1B0H Kd = 0.2 uM LYS ALN LYS n/a n/a
11 1B46 Kd = 5200 nM LYS PRO LYS n/a n/a
12 1B4Z Kd = 5900 nM LYS ASP LYS n/a n/a
13 1B3L Kd = 1300 nM LYS GLY LYS n/a n/a
14 1QKA Kd = 1200 nM LYS ARG LYS n/a n/a
15 1B3F Kd = 130 nM LYS HIS LYS n/a n/a
16 1B52 Kd = 76 nM LYS THR LYS n/a n/a
17 1OLA - VAL LYS PRO GLY n/a n/a
18 1B2H Kd = 29 uM LYS ORN LYS n/a n/a
19 1B4H Kd = 3.44 uM LYS DAB LYS n/a n/a
20 1B9J Kd = 1100 nM LYS LEU LYS n/a n/a
21 1OLC Kd = 2.7 uM LYS LYS LYS ALA n/a n/a
22 1B3H Kd = 0.62 uM LYS ALC LYS n/a n/a
23 1JEU Kd = 150 nM LYS GLU LYS n/a n/a
24 2RKM Ki = 125 uM LYS LYS n/a n/a
25 1B51 Kd = 43 nM LYS SER LYS n/a n/a
26 1B58 Kd = 260 nM LYS TYR LYS n/a n/a
27 1JEV Kd = 130 nM LYS TRP LYS n/a n/a
28 1QKB Kd = 45 nM LYS VAL LYS n/a n/a
29 1B1H Kd = 0.093 uM LYS HPE LYS n/a n/a
30 1B32 Kd = 79 nM LYS MET LYS n/a n/a
31 1B05 Kd = 75 nM LYS CYS LYS n/a n/a
32 6DQT - LEU GLY GLY n/a n/a
33 6DTG - TYR LEU GLY ALA ASN GLY n/a n/a
34 6DQR - MET GLY GLY n/a n/a
35 6DTH - ARG PRO PRO GLY PHE n/a n/a
36 6DQQ - ALA ALA ALA ALA n/a n/a
37 6DQU - GLY ILE ILE ASN THR LEU n/a n/a
38 6DTF - LYS LYS LYS n/a n/a
39 3TCG Kd = 1.36 uM LYS GLY GLU n/a n/a
40 2Z23 - LYS LYS LYS n/a n/a
50% Homology Family (41)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 165 families.
1 3O9P Kd = 0.3 uM MHI C15 H26 N4 O8 C[C@@H](C(....
2 1B5H Kd = 0.97 uM LYS DPP LYS n/a n/a
3 1B3G Kd = 200 nM LYS ILE LYS n/a n/a
4 1B40 Kd = 53 nM LYS PHE LYS n/a n/a
5 1JET Kd = 56 nM LYS ALA LYS n/a n/a
6 1B5I Kd = 90 nM LYS ASN LYS n/a n/a
7 1B5J Kd = 37 nM LYS GLN LYS n/a n/a
8 2OLB Kd = 2900 nM LYS LYS LYS n/a n/a
9 1B6H Kd = 0.015 uM LYS NVA LYS n/a n/a
10 1B7H Kd = 0.0095 uM LYS NLE LYS n/a n/a
11 1B0H Kd = 0.2 uM LYS ALN LYS n/a n/a
12 1B46 Kd = 5200 nM LYS PRO LYS n/a n/a
13 1B4Z Kd = 5900 nM LYS ASP LYS n/a n/a
14 1B3L Kd = 1300 nM LYS GLY LYS n/a n/a
15 1QKA Kd = 1200 nM LYS ARG LYS n/a n/a
16 1B3F Kd = 130 nM LYS HIS LYS n/a n/a
17 1B52 Kd = 76 nM LYS THR LYS n/a n/a
18 1OLA - VAL LYS PRO GLY n/a n/a
19 1B2H Kd = 29 uM LYS ORN LYS n/a n/a
20 1B4H Kd = 3.44 uM LYS DAB LYS n/a n/a
21 1B9J Kd = 1100 nM LYS LEU LYS n/a n/a
22 1OLC Kd = 2.7 uM LYS LYS LYS ALA n/a n/a
23 1B3H Kd = 0.62 uM LYS ALC LYS n/a n/a
24 1JEU Kd = 150 nM LYS GLU LYS n/a n/a
25 2RKM Ki = 125 uM LYS LYS n/a n/a
26 1B51 Kd = 43 nM LYS SER LYS n/a n/a
27 1B58 Kd = 260 nM LYS TYR LYS n/a n/a
28 1JEV Kd = 130 nM LYS TRP LYS n/a n/a
29 1QKB Kd = 45 nM LYS VAL LYS n/a n/a
30 1B1H Kd = 0.093 uM LYS HPE LYS n/a n/a
31 1B32 Kd = 79 nM LYS MET LYS n/a n/a
32 1B05 Kd = 75 nM LYS CYS LYS n/a n/a
33 6DQT - LEU GLY GLY n/a n/a
34 6DTG - TYR LEU GLY ALA ASN GLY n/a n/a
35 6DQR - MET GLY GLY n/a n/a
36 6DTH - ARG PRO PRO GLY PHE n/a n/a
37 6DQQ - ALA ALA ALA ALA n/a n/a
38 6DQU - GLY ILE ILE ASN THR LEU n/a n/a
39 6DTF - LYS LYS LYS n/a n/a
40 3TCG Kd = 1.36 uM LYS GLY GLU n/a n/a
41 2Z23 - LYS LYS LYS n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: ARG PRO PRO GLY PHE; Similar ligands found: 36
No: Ligand ECFP6 Tc MDL keys Tc
1 ARG PRO PRO GLY PHE 1 1
2 ARG PRO PRO GLY PHE SER PRO PHE ARG 1 1
3 ARG PRO PRO GLY PHE SER PRO PHE ALA 0.651163 0.876923
4 PHE PRO ARG 0.559633 0.912281
5 ARG PRO GLY ASN PHE LEU GLN SER ARG LEU 0.516556 0.823529
6 ARG PRO PRO LYS PRO ARG PRO ARG 0.516393 0.929825
7 ARG PRO PRO ILE PHE ILE ARG ARG LEU 0.510791 0.875
8 DPN PRO ARG 0.504425 0.881356
9 ARG PRO GLY ASN PHE LEU GLN SER ARG PRO 0.48 0.811594
10 DPN PRO DAR CYS NH2 0.479339 0.898305
11 DPN PRO DAR DTH NH2 0.456 0.828125
12 DPN PRO DAR ILE NH2 0.456 0.868852
13 01B PRO PRO ALA NH2 0.451327 0.765625
14 ILE ARG ALA ALA PRO PRO PRO LEU PHE 0.448276 0.861538
15 VAL PRO PRO PRO ARG PRO PRO PRO PRO GLU 0.444444 0.885246
16 0G6 0.436975 0.870968
17 ACE PRO PRO PRO VAL PRO PRO ARG ARG ARG 0.434426 0.854839
18 ARG SEP PRO VAL PHE SER 0.431507 0.760563
19 ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 0.43038 0.823529
20 ACE PRO ALA PRO PHE ALA ALA ALA ALA NH2 0.429825 0.754098
21 PHE ASN ARG PRO VAL 0.425373 0.830769
22 ILE GLY PRO GLY ARG ALA PHE TYR ALA 0.424837 0.797101
23 ARG PRO MET THR PHE LYS GLY ALA LEU 0.423313 0.753425
24 GLU PRO GLY GLY SER ARG 0.418605 0.828125
25 GLY PHE ARG PRO 0.418033 0.915254
26 ACE GLY PHE GLY VAL VAL PRO SER PHE TYR 0.416058 0.691176
27 ALA PRO PRO PRO ARG PRO PRO LYS PRO 0.407692 0.898305
28 ASN TYR THR PRO GLY PRO GLY THR ARG PHE 0.407407 0.802817
29 ILE GLY PRO GLY ARG ALA PHE TYR THR 0.405063 0.785714
30 ILE GLY PRO GLY ARG ALA PHE TYR VAL 0.405063 0.785714
31 MAA LYS PRO PHE 0.404762 0.8
32 PRO ALA PRO PHE PRO ALA NH2 0.403361 0.830508
33 ARG ILE PRO SER TYR ARG TYR ARG TYR 0.402778 0.777778
34 ARG GLY PRO GLY CYS ALA PHE VAL THR ILE 0.401235 0.785714
35 ASP LEU PRO PHE 0.4 0.734375
36 ASN TYR THR PRO GLY PRO GLY ILE ARG PHE 0.4 0.780822
Similar Ligands (3D)
Ligand no: 1; Ligand: ARG PRO PRO GLY PHE; 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 : 6DQU; Ligand: GLY ILE ILE ASN THR LEU; 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: 6dqu.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
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