scPDB - 2gd0 entry

Protein Data Bank Entry:

PDB ID : 2gd0

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2006-03-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Probable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase )
ID:	O06543_MYCTU
AC:	O06543
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	25 %
B	75 %

Ligand binding site composition:

B-Factor:	26.057
Number of residues:	62
Including
Standard Amino Acids:	59
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.336	1022.625

% Hydrophobic	% Polar
50.83	49.17
According to VolSite

Ligand :

HET Code:	MRS
Formula:	C36H60N7O17P3S
Molecular weight:	987.885 g/mol
DrugBank ID:	-
Buried Surface Area:	52.63 %
Polar Surface area:	429.68 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	32

Mass center Coordinates

X	Y	Z
50.6048	-51.1127	-23.413

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
C4	CG2	ILE- 16	3.71	0	Hydrophobic	false
C14	CB	ASP- 48	4.19	0	Hydrophobic	false
N6A	O	ALA- 59	3.36	176.31	H-Bond (Ligand Donor)	false
N1A	N	LEU- 61	3.12	156.52	H-Bond (Protein Donor)	false
O9A	NZ	LYS- 62	3.27	169.18	H-Bond (Protein Donor)	false
O9A	NZ	LYS- 62	3.27	0	Ionic (Protein Cationic)	false
N8P	O	GLY- 83	3.21	134.41	H-Bond (Ligand Donor)	false
C5B	CD2	TYR- 84	4.34	0	Hydrophobic	false
O1A	CZ	ARG- 85	3.06	0	Ionic (Protein Cationic)	false
O1A	NE	ARG- 85	2.71	121.95	H-Bond (Protein Donor)	false
O2A	N	ARG- 85	3.11	169.04	H-Bond (Protein Donor)	false
C5B	CG1	VAL- 88	4.37	0	Hydrophobic	false
C2B	CG1	VAL- 88	3.5	0	Hydrophobic	false
O7A	CZ	ARG- 91	4	0	Ionic (Protein Cationic)	false
C2B	CD1	LEU- 92	4.49	0	Hydrophobic	false
CEP	CB	ALA- 124	4.31	0	Hydrophobic	false
N4P	O	GLY- 125	3.48	125.46	H-Bond (Ligand Donor)	false
C13	CB	HIS- 126	3.99	0	Hydrophobic	false
O1	N	ASP- 127	2.82	149.54	H-Bond (Protein Donor)	false
C13	CB	ASP- 127	4.37	0	Hydrophobic	false
C6P	CZ	TYR- 130	4.43	0	Hydrophobic	false
C2P	CE2	TYR- 130	4.4	0	Hydrophobic	false
N4P	OH	TYR- 130	3.17	160.84	H-Bond (Ligand Donor)	false
C13	CB	ASN- 152	4.16	0	Hydrophobic	false
C6P	CE	MET- 188	4.16	0	Hydrophobic	false
C2P	CE	MET- 188	3.82	0	Hydrophobic	false
C10	SD	MET- 202	4.14	0	Hydrophobic	false
C12	CG	MET- 202	3.66	0	Hydrophobic	false
C15	CG2	THR- 205	3.93	0	Hydrophobic	false
C10	CE	MET- 207	3.84	0	Hydrophobic	false
C12	CE	MET- 207	3.84	0	Hydrophobic	false
C14	SD	MET- 207	3.69	0	Hydrophobic	false
C13	CD2	LEU- 217	3.95	0	Hydrophobic	false
C5	CD1	LEU- 217	3.94	0	Hydrophobic	false
C13	CE1	TYR- 224	4.08	0	Hydrophobic	false
C5	CD1	ILE- 240	4.33	0	Hydrophobic	false
C13	CD1	ILE- 240	4.09	0	Hydrophobic	false
CEP	CZ	PHE- 244	4.19	0	Hydrophobic	false