scPDB - 3u7k entry

Protein Data Bank Entry:

PDB ID : 3u7k

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2011-10-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Peptide deformylase
ID:	DEF_STAAC
AC:	Q5HGZ3
Organism:	Staphylococcus aureus
Reign:	Bacteria
TaxID:	93062
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	15.447
Number of residues:	34
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.292	300.375

% Hydrophobic	% Polar
42.70	57.30
According to VolSite

Ligand :

HET Code:	MDB
Formula:	C22H34N4O5
Molecular weight:	434.529 g/mol
DrugBank ID:	-
Buried Surface Area:	63.13 %
Polar Surface area:	120 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	2
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-15.8424	84.7383	70.2786

Binding mode :

What is Poseview ?

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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
CAQ	CG	GLN- 45	3.64	0	Hydrophobic	false
CAC	CB	ARG- 56	4	0	Hydrophobic	false
N	O	SER- 57	2.94	152.06	H-Bond (Ligand Donor)	false
NAI	O	SER- 57	3.14	143.56	H-Bond (Ligand Donor)	false
OAP	OG	SER- 57	2.94	166.53	H-Bond (Protein Donor)	false
CAQ	CB	SER- 57	4.28	0	Hydrophobic	false
O	N	VAL- 59	3.04	151.75	H-Bond (Protein Donor)	false
CAK	CG1	VAL- 59	4.26	0	Hydrophobic	false
CAQ	CG1	VAL- 59	3.6	0	Hydrophobic	false
CAP	CG1	VAL- 59	3.71	0	Hydrophobic	false
CBD	CG2	VAL- 59	4.23	0	Hydrophobic	false
OAX	NE2	GLN- 65	2.95	122.3	H-Bond (Protein Donor)	false
CBB	CD1	LEU- 105	4.08	0	Hydrophobic	false
CBA	CB	GLU- 109	3.95	0	Hydrophobic	false
CBB	CG	GLU- 109	3.56	0	Hydrophobic	false
CAC	CD2	LEU- 112	3.7	0	Hydrophobic	false
OAV	N	LEU- 112	2.8	163.49	H-Bond (Protein Donor)	false
CBC	CG2	VAL- 151	4.05	0	Hydrophobic	false
CBC	CB	HIS- 154	3.92	0	Hydrophobic	false
CAL	CG	GLU- 185	3.59	0	Hydrophobic	false
OAX	ZN	ZN- 350	2.13	0	Metal Acceptor	false