scPDB - 4cuk entry

Protein Data Bank Entry:

PDB ID : 4cuk

Resolution :2.180 Å

Experimental Method : X-ray

Deposition Date : 2014-03-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	D-lactate dehydrogenase
ID:	Q8Z780_SALTI
AC:	Q8Z780
Organism:	Salmonella typhi
Reign:	Bacteria
TaxID:	90370
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	22.586
Number of residues:	43
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.928	725.625

% Hydrophobic	% Polar
50.23	49.77
According to VolSite

Ligand :

HET Code:	NAI
Formula:	C21H27N7O14P2
Molecular weight:	663.425 g/mol
DrugBank ID:	DB00157
Buried Surface Area:	56.31 %
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
81.955	43.068	193.314

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
C4N	CE2	TYR- 100	3.71	0	Hydrophobic	false
C4N	CG2	VAL- 105	3.57	0	Hydrophobic	false
C4N	CD1	ILE- 155	4.37	0	Hydrophobic	false
C5D	CD1	ILE- 155	3.91	0	Hydrophobic	false
O2N	N	ILE- 155	3.03	157.66	H-Bond (Protein Donor)	false
O3B	OD2	ASP- 174	2.81	169.59	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 174	2.93	162.04	H-Bond (Ligand Donor)	false
C1B	CB	CYS- 205	4.4	0	Hydrophobic	false
C3D	CG	PRO- 206	4.24	0	Hydrophobic	false
C5B	CG	PRO- 206	3.6	0	Hydrophobic	false
N7N	O	THR- 232	2.73	134.19	H-Bond (Ligand Donor)	false
C1D	CB	SER- 233	4.16	0	Hydrophobic	false
O4D	OG	SER- 233	3.11	157.97	H-Bond (Protein Donor)	false
N7N	OD2	ASP- 258	3.17	140.66	H-Bond (Ligand Donor)	false
O7N	NE2	HIS- 295	2.72	127.24	H-Bond (Protein Donor)	false
O2N	O	HOH- 2065	2.68	179.98	H-Bond (Protein Donor)	false
O2D	O	HOH- 2086	2.77	161.06	H-Bond (Ligand Donor)	false