scPDB - 4okn entry

Protein Data Bank Entry:

PDB ID : 4okn

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2014-01-22

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 A chain
ID:	LDHA_HUMAN
AC:	P00338
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.1.1.27

Chains:

Chain Name:	Percentage of Residues within binding site
A	90 %
G	10 %

Ligand binding site composition:

B-Factor:	37.297
Number of residues:	53
Including
Standard Amino Acids:	51
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.962	1603.125

% Hydrophobic	% Polar
40.42	59.58
According to VolSite

Ligand :

HET Code:	NAI
Formula:	C21H27N7O14P2
Molecular weight:	663.425 g/mol
DrugBank ID:	DB00157
Buried Surface Area:	73.63 %
Polar Surface area:	342.9 Å2

Number of
H-Bond Acceptors:	19
H-Bond Donors:	6
Rings:	5
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
27.5605	-2.32289	-28.4266

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
O2A	N	ALA- 30	3.03	161.47	H-Bond (Protein Donor)	false
O1N	N	VAL- 31	2.89	162.88	H-Bond (Protein Donor)	false
C5D	CG2	VAL- 31	4.01	0	Hydrophobic	false
C1D	CG2	VAL- 31	4.47	0	Hydrophobic	false
O3B	OD2	ASP- 52	2.64	160.88	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 52	2.73	149.47	H-Bond (Ligand Donor)	false
O2B	OD2	ASP- 52	3.48	130.49	H-Bond (Ligand Donor)	false
C2B	CD1	ILE- 54	4.36	0	Hydrophobic	false
C1B	CB	ALA- 96	4.2	0	Hydrophobic	false
O4B	N	GLY- 97	3.2	156.46	H-Bond (Protein Donor)	false
O3D	O	ALA- 98	2.53	155.67	H-Bond (Ligand Donor)	false
O2N	CZ	ARG- 99	3.84	0	Ionic (Protein Cationic)	false
O2N	NH1	ARG- 99	2.87	165.72	H-Bond (Protein Donor)	false
C2D	CB	ARG- 99	3.51	0	Hydrophobic	false
N6A	OD1	ASN- 108	3.06	138.04	H-Bond (Ligand Donor)	false
N7N	O	VAL- 136	2.89	177.85	H-Bond (Ligand Donor)	false
O3D	N	ASN- 138	3.21	169.26	H-Bond (Protein Donor)	false
O2D	ND2	ASN- 138	3	132.65	H-Bond (Protein Donor)	false
C1D	CB	ASN- 138	4.34	0	Hydrophobic	false
N7N	OG	SER- 161	3.18	120.35	H-Bond (Ligand Donor)	false
C4N	CB	ILE- 252	3.68	0	Hydrophobic	false