scPDB - 4rkd entry

Protein Data Bank Entry:

PDB ID : 4rkd

Resolution :2.760 Å

Experimental Method : X-ray

Deposition Date : 2014-10-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Aminotransferase
ID:	C7E5X4_9GAMM
AC:	C7E5X4
Organism:	Psychrobacter sp. B6
Reign:	Bacteria
TaxID:	408968
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
G	87 %
H	13 %

Ligand binding site composition:

B-Factor:	37.394
Number of residues:	40
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.020	1120.500

% Hydrophobic	% Polar
52.11	47.89
According to VolSite

Ligand :

HET Code:	KET
Formula:	C12H11N2O9P
Molecular weight:	358.197 g/mol
DrugBank ID:	-
Buried Surface Area:	71.76 %
Polar Surface area:	207.97 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	1
Rings:	1
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
32.393	68.6378	163.008

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
OP2	OG	SER- 104	2.62	146.2	H-Bond (Protein Donor)	false
OP2	N	SER- 104	3.06	147.82	H-Bond (Protein Donor)	false
C2A	CE3	TRP- 130	4.16	0	Hydrophobic	false
C5A	CH2	TRP- 130	3.57	0	Hydrophobic	false
CA	CE2	TRP- 130	3.72	0	Hydrophobic	false
OD1	NE1	TRP- 130	2.86	140.84	H-Bond (Protein Donor)	false
C2A	CB	ASN- 183	4.49	0	Hydrophobic	false
O3	ND2	ASN- 183	2.66	141.45	H-Bond (Protein Donor)	false
N1	OD2	ASP- 211	2.9	154.47	H-Bond (Protein Donor)	false
C2A	CB	ALA- 213	4.3	0	Hydrophobic	false
C2A	CE2	TYR- 214	4.32	0	Hydrophobic	false
OP1	OG	SER- 243	2.67	144.44	H-Bond (Protein Donor)	false
OP3	OG	SER- 245	3.05	161.27	H-Bond (Protein Donor)	false
CB	CE	LYS- 246	4.49	0	Hydrophobic	false
OP2	CZ	ARG- 254	3.6	0	Ionic (Protein Cationic)	false
OP3	CZ	ARG- 254	3.87	0	Ionic (Protein Cationic)	false
OP3	NH1	ARG- 254	3.25	159.22	H-Bond (Protein Donor)	false
CB	CZ	PHE- 348	4.18	0	Hydrophobic	false
OD2	NH2	ARG- 374	2.76	131.19	H-Bond (Protein Donor)	false
OD2	CZ	ARG- 374	3.02	0	Ionic (Protein Cationic)	false