scPDB - 3ksd entry

Protein Data Bank Entry:

PDB ID : 3ksd

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2009-11-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glyceraldehyde-3-phosphate dehydrogenase 1
ID:	G3P1_STAAR
AC:	Q6GIL8
Organism:	Staphylococcus aureus
Reign:	Bacteria
TaxID:	282458
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
P	7 %
Q	93 %

Ligand binding site composition:

B-Factor:	27.355
Number of residues:	50
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.235	985.500

% Hydrophobic	% Polar
41.10	58.90
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	60.03 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
9.83007	-3.38756	17.9352

Binding mode :

What is Poseview ?

2D View
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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
O2N	N	ILE- 13	3.09	168	H-Bond (Protein Donor)	false
C3N	CG1	ILE- 13	3.64	0	Hydrophobic	false
C4N	CD1	ILE- 13	3.97	0	Hydrophobic	false
C5N	CG1	ILE- 13	4.45	0	Hydrophobic	false
O3B	OD1	ASP- 34	2.63	160.58	H-Bond (Ligand Donor)	false
O3B	OD2	ASP- 34	3.4	120.67	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 34	3.2	156.85	H-Bond (Ligand Donor)	false
O2B	OD2	ASP- 34	2.52	135.02	H-Bond (Ligand Donor)	false
C2B	CD1	LEU- 35	4.4	0	Hydrophobic	false
N6A	O	PRO- 78	3.04	162.39	H-Bond (Ligand Donor)	false
O4D	OG	SER- 120	2.91	147	H-Bond (Protein Donor)	false
C3D	CB	ALA- 121	4.43	0	Hydrophobic	false
C5N	CB	SER- 151	3.77	0	Hydrophobic	false
O7N	ND2	ASN- 316	2.69	175.34	H-Bond (Protein Donor)	false
C5N	CB	TYR- 320	4.3	0	Hydrophobic	false
O2N	O	HOH- 338	2.8	179.96	H-Bond (Protein Donor)	false
O3D	O	HOH- 339	2.84	179.98	H-Bond (Protein Donor)	false
N1A	O	HOH- 407	2.84	179.96	H-Bond (Protein Donor)	false