scPDB - 4nbu entry

Protein Data Bank Entry:

PDB ID : 4nbu

Resolution :1.340 Å

Experimental Method : X-ray

Deposition Date : 2013-10-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	3-oxoacyl-(Acyl-carrier-protein) reductase
ID:	A6CQL2_9BACI
AC:	A6CQL2
Organism:	Bacillus sp. SG-1
Reign:	Bacteria
TaxID:	161544
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	97 %
D	3 %

Ligand binding site composition:

B-Factor:	23.261
Number of residues:	32
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	NAI
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.030	310.500

% Hydrophobic	% Polar
44.57	55.43
According to VolSite

Ligand :

HET Code:	CAA
Formula:	C25H36N7O18P3S
Molecular weight:	847.576 g/mol
DrugBank ID:	DB03059
Buried Surface Area:	41.06 %
Polar Surface area:	446.75 Å2

Number of
H-Bond Acceptors:	23
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	22

Mass center Coordinates

X	Y	Z
57.9686	59.7366	85.9774

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
CDP	CB	ASP- 99	4.11	0	Hydrophobic	false
CEP	CB	ASP- 99	4.11	0	Hydrophobic	false
C6P	CB	ASP- 99	4.49	0	Hydrophobic	false
N4P	OD2	ASP- 99	2.94	151.18	H-Bond (Ligand Donor)	false
CCP	CG	MET- 101	4.28	0	Hydrophobic	false
O5A	NZ	LYS- 104	3.03	148.55	H-Bond (Protein Donor)	false
O5A	NZ	LYS- 104	3.03	0	Ionic (Protein Cationic)	false
C4	CB	THR- 147	4.26	0	Hydrophobic	false
N6A	OD1	ASN- 152	3.4	144.81	H-Bond (Ligand Donor)	false
O5P	ND2	ASN- 152	3.09	131.44	H-Bond (Protein Donor)	false
C1B	CG1	VAL- 153	4.34	0	Hydrophobic	false
O1	NE2	GLN- 155	2.82	157.87	H-Bond (Protein Donor)	false
C2	CZ	TYR- 158	3.85	0	Hydrophobic	false
C4	CE2	TYR- 158	4.18	0	Hydrophobic	false
O3	OH	TYR- 158	2.54	130.74	H-Bond (Protein Donor)	false
C2P	CE1	PHE- 190	3.82	0	Hydrophobic	false
S1P	CD1	PHE- 190	4.49	0	Hydrophobic	false
C4	CE1	PHE- 190	3.4	0	Hydrophobic	false
S1P	CG	MET- 195	4.07	0	Hydrophobic	false
C2	SD	MET- 195	3.56	0	Hydrophobic	false
S1P	CG2	VAL- 196	3.9	0	Hydrophobic	false
C2	C4N	NAI- 301	3.65	0	Hydrophobic	false
C4	C4N	NAI- 301	4.29	0	Hydrophobic	false