scPDB - 3d4p entry

Protein Data Bank Entry:

PDB ID : 3d4p

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2008-05-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	L-lactate dehydrogenase 1
ID:	LDH1_STAAC
AC:	Q5HJD7
Organism:	Staphylococcus aureus
Reign:	Bacteria
TaxID:	93062
EC Number:	1.1.1.27

Chains:

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

Ligand binding site composition:

B-Factor:	13.240
Number of residues:	49
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.173	1009.125

% Hydrophobic	% Polar
44.15	55.85
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	58.36 %
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
23.8528	33.1514	31.3804

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
O1A	N	ALA- 16	3.09	162.12	H-Bond (Protein Donor)	false
O2N	N	VAL- 17	2.81	166.74	H-Bond (Protein Donor)	false
C5D	CG2	VAL- 17	4.24	0	Hydrophobic	false
C5N	CG2	VAL- 17	3.82	0	Hydrophobic	false
O3B	OD1	ASP- 38	2.66	174.38	H-Bond (Ligand Donor)	false
O3B	OD2	ASP- 38	3.29	124.85	H-Bond (Ligand Donor)	false
O2B	OD2	ASP- 38	2.61	157.02	H-Bond (Ligand Donor)	false
C1B	CB	ALA- 82	4.37	0	Hydrophobic	false
O4B	N	GLY- 83	3.25	170.72	H-Bond (Protein Donor)	false
C2D	CB	ALA- 85	4.22	0	Hydrophobic	false
N7N	O	ALA- 122	2.94	150.85	H-Bond (Ligand Donor)	false
C4D	CG2	THR- 123	4.37	0	Hydrophobic	false
O3D	N	ASN- 124	3.04	168.4	H-Bond (Protein Donor)	false
O2D	ND2	ASN- 124	3.14	148.22	H-Bond (Protein Donor)	false
C2D	CB	ASN- 124	4.47	0	Hydrophobic	false
N7N	OG	SER- 147	3.43	131.47	H-Bond (Ligand Donor)	false
C4N	CD2	LEU- 151	4.47	0	Hydrophobic	false
C3N	CG2	VAL- 236	3.86	0	Hydrophobic	false
C4N	CG1	VAL- 236	3.63	0	Hydrophobic	false
O2N	O	HOH- 320	2.71	172	H-Bond (Protein Donor)	false
O3D	O	HOH- 338	2.67	167.31	H-Bond (Ligand Donor)	false