scPDB - 3nfb entry

Protein Data Bank Entry:

PDB ID : 3nfb

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2010-06-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Beta-peptidyl aminopeptidase BapA
ID:	BAPA_SPHXN
AC:	Q52VH2
Organism:	Sphingosinicella xenopeptidilytica
Reign:	Bacteria
TaxID:	364098
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	4 %
B	23 %
D	73 %

Ligand binding site composition:

B-Factor:	15.886
Number of residues:	27
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.371	877.500

% Hydrophobic	% Polar
51.15	48.85
According to VolSite

Ligand :

HET Code:	OAE
Formula:	C16H21N3O5S
Molecular weight:	367.420 g/mol
DrugBank ID:	-
Buried Surface Area:	56.23 %
Polar Surface area:	178.91 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	2
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	2
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
69.3601	0.7916	14.4693

Binding mode :

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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
C8	CG2	THR- 100	3.96	0	Hydrophobic	false
C16	CE1	PHE- 124	3.71	0	Hydrophobic	false
C8	CB	LEU- 127	3.78	0	Hydrophobic	false
C8	CG	LEU- 128	3.95	0	Hydrophobic	false
C9	CD1	LEU- 128	3.83	0	Hydrophobic	false
C11	CD1	LEU- 128	4.2	0	Hydrophobic	false
N2	OE1	GLU- 133	2.77	0	Ionic (Ligand Cationic)	false
N2	OE2	GLU- 133	2.99	0	Ionic (Ligand Cationic)	false
N2	OE2	GLU- 133	2.99	149.64	H-Bond (Ligand Donor)	false
C1	CD2	LEU- 135	3.79	0	Hydrophobic	false
S1	CD2	LEU- 135	4.16	0	Hydrophobic	false
C7	CB	LEU- 135	4.42	0	Hydrophobic	false
C8	CD2	LEU- 135	4.48	0	Hydrophobic	false
O3	N	LEU- 135	2.9	125.72	H-Bond (Protein Donor)	false
N2	OG	SER- 250	3.23	130.54	H-Bond (Ligand Donor)	false
O4	OG	SER- 250	2.66	152.79	H-Bond (Protein Donor)	false
O4	N	SER- 250	2.81	156.94	H-Bond (Protein Donor)	false
N1	O	LEU- 287	2.85	164.56	H-Bond (Ligand Donor)	false
S1	CB	LEU- 287	4.11	0	Hydrophobic	false
C16	CD1	LEU- 287	3.65	0	Hydrophobic	false
N2	O	HOH- 407	2.8	128.28	H-Bond (Ligand Donor)	false