scPDB - 4n9w entry

Protein Data Bank Entry:

PDB ID : 4n9w

Resolution :1.940 Å

Experimental Method : X-ray

Deposition Date : 2013-10-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Phosphatidyl-myo-inositol mannosyltransferase
ID:	PIMA_MYCS2
AC:	A0QWG6
Organism:	Mycobacterium smegmatis 155)
Reign:	Bacteria
TaxID:	246196
EC Number:	2.4.1.57

Chains:

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

Ligand binding site composition:

B-Factor:	32.828
Number of residues:	34
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.149	1454.625

% Hydrophobic	% Polar
44.55	55.45
According to VolSite

Ligand :

HET Code:	GDP
Formula:	C10H12N5O11P2
Molecular weight:	440.177 g/mol
DrugBank ID:	DB04315
Buried Surface Area:	54.15 %
Polar Surface area:	276.39 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
6.56861	7.01771	16.4823

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
C1'	CB	PRO- 14	4.29	0	Hydrophobic	false
O1B	N	GLY- 16	3.01	177.04	H-Bond (Protein Donor)	false
C2'	CD2	LEU- 194	3.74	0	Hydrophobic	false
O2B	NZ	LYS- 202	3.65	0	Ionic (Protein Cationic)	false
N1	O	VAL- 251	2.98	140.59	H-Bond (Ligand Donor)	false
N2	O	VAL- 251	2.94	142.1	H-Bond (Ligand Donor)	false
N2	OD1	ASP- 253	2.97	154.13	H-Bond (Ligand Donor)	false
C2'	CD	LYS- 256	4.33	0	Hydrophobic	false
O2'	NZ	LYS- 256	2.95	161.58	H-Bond (Protein Donor)	false
C3'	CG2	ILE- 278	3.61	0	Hydrophobic	false
C5'	CG2	VAL- 279	4.16	0	Hydrophobic	false
C2'	CG2	VAL- 279	3.81	0	Hydrophobic	false
O3'	OE2	GLU- 282	2.85	167.69	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 282	3.21	135.62	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 282	2.65	154.64	H-Bond (Ligand Donor)	false
O1B	O	HOH- 507	3.41	135.37	H-Bond (Protein Donor)	false
O1A	O	HOH- 515	2.5	179.96	H-Bond (Protein Donor)	false