scPDB - 2yim entry

Protein Data Bank Entry:

PDB ID : 2yim

Resolution :1.410 Å

Experimental Method : X-ray

Deposition Date : 2011-05-16

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
C	80 %
D	20 %

Ligand binding site composition:

B-Factor:	12.303
Number of residues:	54
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.122	870.750

% Hydrophobic	% Polar
49.61	50.39
According to VolSite

Ligand :

HET Code:	MC4
Formula:	C26H38N7O18P3S
Molecular weight:	861.602 g/mol
DrugBank ID:	-
Buried Surface Area:	59.62 %
Polar Surface area:	449.91 Å2

Number of
H-Bond Acceptors:	23
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	21

Mass center Coordinates

X	Y	Z
117.642	24.1178	40.0434

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	CD1	ILE- 16	3.84	0	Hydrophobic	false
S1P	CD1	ILE- 16	3.78	0	Hydrophobic	false
C2P	CG1	ILE- 16	4.4	0	Hydrophobic	false
CDP	CD1	ILE- 16	3.98	0	Hydrophobic	false
O4B	NH2	ARG- 38	3.38	133.72	H-Bond (Protein Donor)	false
N6A	O	ALA- 59	2.99	161.26	H-Bond (Ligand Donor)	false
N1A	N	LEU- 61	3.06	161.79	H-Bond (Protein Donor)	false
O9A	NZ	LYS- 62	2.82	143.05	H-Bond (Protein Donor)	false
O9A	NZ	LYS- 62	2.82	0	Ionic (Protein Cationic)	false
N8P	O	GLY- 83	3.13	132.83	H-Bond (Ligand Donor)	false
C5B	CD1	TYR- 84	4.18	0	Hydrophobic	false
O1A	N	ARG- 85	3.17	167.33	H-Bond (Protein Donor)	false
O2A	NE	ARG- 85	2.64	141.61	H-Bond (Protein Donor)	false
O4A	NH2	ARG- 85	2.85	164.46	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 85	3.64	0	Ionic (Protein Cationic)	false
O4A	CZ	ARG- 85	3.74	0	Ionic (Protein Cationic)	false
CAP	CG	ARG- 85	3.86	0	Hydrophobic	false
C5B	CG1	VAL- 88	4.28	0	Hydrophobic	false
C2B	CG1	VAL- 88	3.61	0	Hydrophobic	false
O7A	NE	ARG- 91	3.29	141.56	H-Bond (Protein Donor)	false
O7A	NH2	ARG- 91	2.93	159.98	H-Bond (Protein Donor)	false
O7A	CZ	ARG- 91	3.55	0	Ionic (Protein Cationic)	false
C2B	CD1	LEU- 92	4.39	0	Hydrophobic	false
CEP	CB	ALA- 124	3.75	0	Hydrophobic	false
N4P	O	GLY- 125	3.31	122.99	H-Bond (Ligand Donor)	false
C52	CB	HIS- 126	3.85	0	Hydrophobic	false
O1	N	ASP- 127	2.88	148.3	H-Bond (Protein Donor)	false
C52	CB	ASP- 127	4.12	0	Hydrophobic	false
N4P	OH	TYR- 130	3.19	161.23	H-Bond (Ligand Donor)	false
C6P	CZ	TYR- 130	4.35	0	Hydrophobic	false
C52	CB	ASN- 152	4.15	0	Hydrophobic	false
C2P	CE	MET- 188	4.22	0	Hydrophobic	false
C6P	CE	MET- 188	4.13	0	Hydrophobic	false
C52	CD2	LEU- 217	4.01	0	Hydrophobic	false
C52	CE2	TYR- 224	4.01	0	Hydrophobic	false
C52	CD1	ILE- 240	4.2	0	Hydrophobic	false
CCP	CZ	PHE- 244	4.38	0	Hydrophobic	false
CEP	CZ	PHE- 244	3.99	0	Hydrophobic	false
O5P	O	HOH- 2023	2.9	179.94	H-Bond (Protein Donor)	false