scPDB - 4f97 entry

Protein Data Bank Entry:

PDB ID : 4f97

Resolution :2.110 Å

Experimental Method : X-ray

Deposition Date : 2012-05-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative glycosyltransferase
ID:	Q15JG1_STRHY
AC:	Q15JG1
Organism:	Streptomyces hygroscopicus subsp. limoneus
Reign:	Bacteria
TaxID:	264445
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	33.066
Number of residues:	29
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	GDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.860	1080.000

% Hydrophobic	% Polar
34.38	65.63
According to VolSite

Ligand :

HET Code:	VDO
Formula:	C14H25NO11P
Molecular weight:	414.322 g/mol
DrugBank ID:	-
Buried Surface Area:	59.76 %
Polar Surface area:	240.45 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	8
Rings:	2
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
12.2567	-6.85537	1.34933

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
CAV	CH2	TRP- 105	4.15	0	Hydrophobic	false
CAB	CZ3	TRP- 105	3.98	0	Hydrophobic	false
OAP	OD2	ASP- 158	2.74	165.51	H-Bond (Ligand Donor)	false
OAO	OD2	ASP- 158	3.25	164.11	H-Bond (Ligand Donor)	false
CAB	CE1	TYR- 159	4.12	0	Hydrophobic	false
OAQ	ND1	HIS- 182	2.85	161.91	H-Bond (Protein Donor)	false
CAB	CG2	ILE- 183	4.11	0	Hydrophobic	false
CAJ	CG2	ILE- 183	4.32	0	Hydrophobic	false
CAH	CE2	PHE- 215	4	0	Hydrophobic	false
CAD	CE2	PHE- 215	3.79	0	Hydrophobic	false
CAG	CD	ARG- 290	3.8	0	Hydrophobic	false
OAY	ND2	ASN- 325	2.66	126.46	H-Bond (Protein Donor)	false
OAW	ND2	ASN- 325	3.3	158.7	H-Bond (Protein Donor)	false
OAY	NH2	ARG- 326	3.32	125.19	H-Bond (Protein Donor)	false
OAY	NE	ARG- 326	2.91	137.62	H-Bond (Protein Donor)	false
OAZ	NH2	ARG- 326	2.84	164.86	H-Bond (Protein Donor)	false
OAY	CZ	ARG- 326	3.5	0	Ionic (Protein Cationic)	false
OAZ	CZ	ARG- 326	3.69	0	Ionic (Protein Cationic)	false
OAS	OD1	ASP- 383	2.65	144.51	H-Bond (Ligand Donor)	false
OAS	N	GLN- 385	3.01	168.15	H-Bond (Protein Donor)	false
CAH	CB	GLN- 385	3.95	0	Hydrophobic	false
OAS	N	ASN- 386	3.46	122.59	H-Bond (Protein Donor)	false
OAR	N	ASN- 386	2.86	160.59	H-Bond (Protein Donor)	false
CAD	CG	LEU- 387	3.92	0	Hydrophobic	false
NAN	O3B	GDP- 501	2.72	147.05	H-Bond (Ligand Donor)	false
OAT	O2B	GDP- 501	2.75	169.41	H-Bond (Ligand Donor)	false
OAR	O2A	GDP- 501	2.75	158.47	H-Bond (Ligand Donor)	false
NAN	O3B	GDP- 501	2.72	0	Ionic (Ligand Cationic)	false
NAN	O2B	GDP- 501	3.65	0	Ionic (Ligand Cationic)	false
OAT	O	HOH- 804	2.88	150.45	H-Bond (Protein Donor)	false