scPDB - 4o9k entry

Protein Data Bank Entry:

PDB ID : 4o9k

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2014-01-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Arabinose 5-phosphate isomerase
ID:	Q60AU8_METCA
AC:	Q60AU8
Organism:	Methylococcus capsulatus
Reign:	Bacteria
TaxID:	243233
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	28 %
B	72 %

Ligand binding site composition:

B-Factor:	16.381
Number of residues:	35
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.886	1069.875

% Hydrophobic	% Polar
36.59	63.41
According to VolSite

Ligand :

HET Code:	CMK
Formula:	C17H24N3O15P
Molecular weight:	541.357 g/mol
DrugBank ID:	DB04482
Buried Surface Area:	61.24 %
Polar Surface area:	307.05 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	7
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
15.6744	-2.07697	8.05958

Binding mode :

What is Poseview ?

2D View
3D View

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
O7	O	LYS- 238	2.77	161.46	H-Bond (Ligand Donor)	false
C2'	CG2	VAL- 255	4.37	0	Hydrophobic	false
C2'	CG2	THR- 257	3.85	0	Hydrophobic	false
O1A	OG1	THR- 257	2.94	142.1	H-Bond (Protein Donor)	false
O2'	OD1	ASP- 260	3.37	122.49	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 260	2.64	167.89	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 260	2.62	157.27	H-Bond (Ligand Donor)	false
O1Y	CZ	ARG- 262	3.88	0	Ionic (Protein Cationic)	false
O1Y	NH2	ARG- 262	2.75	143.73	H-Bond (Protein Donor)	false
O3'	NH1	ARG- 263	3.49	120.79	H-Bond (Protein Donor)	false
O1A	NH1	ARG- 263	2.72	153.02	H-Bond (Protein Donor)	false
O1X	NH2	ARG- 263	3.3	136.75	H-Bond (Protein Donor)	false
O1Y	NH2	ARG- 263	2.97	162.22	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 263	3.79	0	Ionic (Protein Cationic)	false
O1Y	CZ	ARG- 263	3.91	0	Ionic (Protein Cationic)	false
C1'	CG2	THR- 281	4.26	0	Hydrophobic	false
C2'	CB	THR- 281	4.38	0	Hydrophobic	false
O2'	OG1	THR- 281	2.73	161.42	H-Bond (Protein Donor)	false
O3'	OG1	THR- 281	3.32	123.09	H-Bond (Protein Donor)	false
N3C	N	VAL- 285	2.86	163.98	H-Bond (Protein Donor)	false
O2C	N	VAL- 285	3.47	138.54	H-Bond (Protein Donor)	false
N4C	O	VAL- 285	2.82	174.87	H-Bond (Ligand Donor)	false
C8	CB	ARG- 304	4.27	0	Hydrophobic	false
O8	NH1	ARG- 304	2.61	133.88	H-Bond (Protein Donor)	false
C1'	CG2	ILE- 305	4.45	0	Hydrophobic	false
C5'	CG2	ILE- 305	4.08	0	Hydrophobic	false
O2A	ND2	ASN- 306	3.12	162.59	H-Bond (Protein Donor)	false
O5	ND2	ASN- 306	3.2	149.85	H-Bond (Protein Donor)	false
N4C	O	ALA- 307	3.01	158.5	H-Bond (Ligand Donor)	false
O7	ND2	ASN- 320	3.03	139.6	H-Bond (Protein Donor)	false