Receptor
PDB id Resolution Class Description Source Keywords
6H2Q 1.78 Å EC: 3.4.13.9 CRYSTAL STRUCTURE OF ARG184GLN MUTANT OF HUMAN PROLIDASE WIT AND LEUPRO LIGAND HOMO SAPIENS PROLIDASE PEPTIDASE HYDROLYSIS PITA-BREAD METALLOENZYMEMUTATION HYDROLASE
Ref.: STRUCTURAL BASIS FOR PROLIDASE DEFICIENCY DISEASE MECHANISMS. FEBS J. V. 285 3422 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
LEU PRO A:503;
A:506;
B:503;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
227.284 n/a O=C(C...
MN B:500;
B:499;
A:500;
A:499;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
54.938 Mn [Mn+2...
GOL A:504;
A:503;
A:505;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
PRO LEU A:507;
Valid;
none;
submit data
n/a n/a
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5M4Q 1.73 Å EC: 3.4.13.9 CRYSTAL STRUCTURE OF WILD-TYPE HUMAN PROLIDASE WITH MN IONS LIGAND HOMO SAPIENS PROLIDASE PEPTIDASE HYDROLYSIS PITA-BREAD METALLOENZYMEHYDROLASE
Ref.: SUBSTRATE SPECIFICITY AND REACTION MECHANISM OF HUM PROLIDASE. FEBS J. V. 284 2870 2017
Members (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 6SRF - GLY PRO n/a n/a
2 5MC1 - GLY PRO n/a n/a
3 6H2Q - PRO LEU n/a n/a
4 5MBZ - GLY PRO n/a n/a
5 6SRE - GLY PRO n/a n/a
6 5M4J - GLY PRO n/a n/a
7 5MC3 - GLY PRO n/a n/a
8 5MC4 - GLY PRO n/a n/a
9 5MC2 - GLY PRO n/a n/a
10 5MBY - GLY C2 H5 N O2 C(C(=O)O)N
11 5MC5 - GLY PRO n/a n/a
12 5M4L - LEU PRO n/a n/a
13 5M4Q Ki = 0.31 mM PRO C5 H9 N O2 C1C[C@H](N....
14 5MC0 - GLY PRO n/a n/a
70% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 6SRF - GLY PRO n/a n/a
2 5MC1 - GLY PRO n/a n/a
3 6H2Q - PRO LEU n/a n/a
4 5MBZ - GLY PRO n/a n/a
5 6SRE - GLY PRO n/a n/a
6 5M4J - GLY PRO n/a n/a
7 5MC3 - GLY PRO n/a n/a
8 5MC4 - GLY PRO n/a n/a
9 5MC2 - GLY PRO n/a n/a
10 5MBY - GLY C2 H5 N O2 C(C(=O)O)N
11 5MC5 - GLY PRO n/a n/a
12 5M4L - LEU PRO n/a n/a
13 5M4Q Ki = 0.31 mM PRO C5 H9 N O2 C1C[C@H](N....
14 5MC0 - GLY PRO n/a n/a
50% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 6SRF - GLY PRO n/a n/a
2 5MC1 - GLY PRO n/a n/a
3 6H2Q - PRO LEU n/a n/a
4 5MBZ - GLY PRO n/a n/a
5 6SRE - GLY PRO n/a n/a
6 5M4J - GLY PRO n/a n/a
7 5MC3 - GLY PRO n/a n/a
8 5MC4 - GLY PRO n/a n/a
9 5MC2 - GLY PRO n/a n/a
10 5MBY - GLY C2 H5 N O2 C(C(=O)O)N
11 5MC5 - GLY PRO n/a n/a
12 5M4L - LEU PRO n/a n/a
13 5M4Q Ki = 0.31 mM PRO C5 H9 N O2 C1C[C@H](N....
14 5MC0 - GLY PRO n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: LEU PRO; Similar ligands found: 11
No: Ligand ECFP6 Tc MDL keys Tc
1 LEU PRO 1 1
2 SER PRO 0.645833 0.777778
3 ALA PRO 0.630435 0.87234
4 LYS PRO 0.553571 0.823529
5 HIS PRO 0.484375 0.763636
6 31U 0.478873 0.736842
7 21U 0.472222 0.736842
8 GLY PRO 0.45098 0.836735
9 LEU PRO GLU THR GLY 0.433735 0.807018
10 ARG ALA ILE SEP LEU PRO 0.4125 0.741935
11 VAL PRO LEU 0.409091 0.938776
Ligand no: 2; Ligand: PRO LEU; Similar ligands found: 0
No: Ligand ECFP6 Tc MDL keys Tc
Similar Ligands (3D)
Ligand no: 1; Ligand: LEU PRO; Similar ligands found: 17
No: Ligand Similarity coefficient
1 ILE VAL 0.8970
2 ASP SER 0.8963
3 G6P 0.8956
4 BG6 0.8855
5 H35 0.8855
6 VAL VAL 0.8837
7 MPP 0.8780
8 NZ9 0.8740
9 BGP 0.8720
10 X8Z 0.8702
11 OSB 0.8697
12 XQI 0.8659
13 ZIP 0.8642
14 FUZ 0.8632
15 KBR 0.8614
16 2KU 0.8565
17 SER THR 0.8538
Ligand no: 2; Ligand: PRO LEU; Similar ligands found: 30
No: Ligand Similarity coefficient
1 PRO LEU 1.0000
2 ALA LEU 0.9292
3 RDM 0.9099
4 PAL 0.9084
5 6PR 0.9051
6 AAG 0.8993
7 C4L 0.8913
8 6FR 0.8874
9 GLY LEU 0.8820
10 SUO 0.8801
11 2D2 0.8759
12 TCO 0.8752
13 78Y 0.8745
14 SN0 0.8740
15 RBV 0.8728
16 VAL VAL 0.8714
17 MMJ 0.8704
18 MN9 0.8682
19 TH4 0.8681
20 4FF 0.8660
21 X6W 0.8656
22 1BY 0.8641
23 ALA GLN 0.8633
24 ADN 0.8603
25 UN3 0.8583
26 RDV 0.8580
27 JGM 0.8578
28 MUK 0.8575
29 SMG 0.8568
30 AEP 0.8556
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5M4Q; Ligand: PRO; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 5m4q.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 5JR6 01B PRO PRO ALA NH2 18.1818
2 6A9T GLY 44.8352
Pocket No.: 2; Query (leader) PDB : 5M4Q; Ligand: PRO; Similar sites found with APoc: 2
This union binding pocket(no: 2) in the query (biounit: 5m4q.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 5JR6 01B PRO PRO ALA NH2 18.1818
2 6A9T GLY 44.8352
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