scPDB - 4gf5 entry

Protein Data Bank Entry:

PDB ID : 4gf5

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2012-08-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	CalS11
ID:	Q8KNF1_MICEC
AC:	Q8KNF1
Organism:	Micromonospora echinospora
Reign:	Bacteria
TaxID:	1877
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
K	5 %
Q	95 %

Ligand binding site composition:

B-Factor:	14.513
Number of residues:	42
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.812	1289.250

% Hydrophobic	% Polar
36.39	63.61
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	78.38 %
Polar Surface area:	212.38 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-29.7092	32.5744	48.5117

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
N	OE2	GLU- 75	3.08	121.25	H-Bond (Ligand Donor)	false
N	OE2	GLU- 75	3.08	0	Ionic (Ligand Cationic)	false
N	O	GLY- 77	2.88	147.76	H-Bond (Ligand Donor)	false
SD	CB	ARG- 79	4.04	0	Hydrophobic	false
CB	CB	ARG- 79	3.59	0	Hydrophobic	false
O	NE	ARG- 82	3.44	124.65	H-Bond (Protein Donor)	false
OXT	NE	ARG- 82	3.06	154.94	H-Bond (Protein Donor)	false
OXT	NH2	ARG- 82	3.18	144.98	H-Bond (Protein Donor)	false
O	CZ	ARG- 82	3.86	0	Ionic (Protein Cationic)	false
OXT	CZ	ARG- 82	3.56	0	Ionic (Protein Cationic)	false
O3'	OD1	ASP- 107	3.24	136.66	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 107	2.7	158.92	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 107	2.59	160.92	H-Bond (Ligand Donor)	false
N3	N	THR- 108	3.42	136.13	H-Bond (Protein Donor)	false
C2'	CD1	PHE- 112	4.04	0	Hydrophobic	false
C3'	CB	PHE- 130	3.91	0	Hydrophobic	false
SD	CD2	PHE- 130	3.83	0	Hydrophobic	false
N6	OD1	ASP- 166	3.02	166.29	H-Bond (Ligand Donor)	false
N1	N	VAL- 167	3.09	163.8	H-Bond (Protein Donor)	false
N	OD2	ASP- 189	2.8	156.84	H-Bond (Ligand Donor)	false
N	OD2	ASP- 189	2.8	0	Ionic (Ligand Cationic)	false
CG	CB	ASP- 189	4.45	0	Hydrophobic	false
C1'	CD2	LEU- 190	4.35	0	Hydrophobic	false
O3'	O	HOH- 418	3.08	179.96	H-Bond (Protein Donor)	false