scPDB - 4gkm entry

Protein Data Bank Entry:

PDB ID : 4gkm

Resolution :1.670 Å

Experimental Method : X-ray

Deposition Date : 2012-08-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Anthranilate phosphoribosyltransferase
ID:	TRPD_MYCTU
AC:	P9WFX5
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	20.826
Number of residues:	23
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.765	884.250

% Hydrophobic	% Polar
41.98	58.02
According to VolSite

Ligand :

HET Code:	683
Formula:	C15H11NO4
Molecular weight:	269.252 g/mol
DrugBank ID:	-
Buried Surface Area:	60.88 %
Polar Surface area:	92.29 Å2

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

Mass center Coordinates

X	Y	Z
-28.0836	-32.478	7.9004

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
C4	CE	MET- 86	3.82	0	Hydrophobic	false
OX1	ND2	ASN- 138	3.41	121.09	H-Bond (Protein Donor)	false
CY5	CB	ALA- 179	3.58	0	Hydrophobic	false
CX2	CG	PRO- 180	3.84	0	Hydrophobic	false
CX1	CB	PRO- 180	3.64	0	Hydrophobic	false
CY5	CB	HIS- 183	4.07	0	Hydrophobic	false
C4	CE2	TYR- 186	4.24	0	Hydrophobic	false
CX3	CB	TYR- 186	4.28	0	Hydrophobic	false
CY3	CE2	TYR- 186	3.27	0	Hydrophobic	false
CX5	CB	ARG- 187	3.69	0	Hydrophobic	false
CY0	CB	ALA- 190	4.04	0	Hydrophobic	false
CX2	CB	ALA- 190	3.61	0	Hydrophobic	false
OX1	CZ	ARG- 193	3.43	0	Ionic (Protein Cationic)	false
OX2	CZ	ARG- 193	3.12	0	Ionic (Protein Cationic)	false
OX2	NH2	ARG- 193	3.02	121.62	H-Bond (Protein Donor)	false
OX1	NH1	ARG- 194	3.49	129.92	H-Bond (Protein Donor)	false
OY2	NH2	ARG- 194	2.88	141.74	H-Bond (Protein Donor)	false
OY2	NH1	ARG- 194	2.92	139.89	H-Bond (Protein Donor)	false
OY2	CZ	ARG- 194	3.32	0	Ionic (Protein Cationic)	false