scPDB - 1vbi entry

Protein Data Bank Entry:

PDB ID : 1vbi

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2004-02-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Malate/L-lactate dehydrogenase family protein
ID:	Q53W84_THET8
AC:	Q53W84
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	11.025
Number of residues:	47
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.865	955.125

% Hydrophobic	% Polar
49.12	50.88
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	51.09 %
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
3.80211	67.488	11.254

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
C4D	CG1	VAL- 41	4.19	0	Hydrophobic	false
N7N	O	GLY- 117	2.94	162.12	H-Bond (Ligand Donor)	false
O2D	N	ALA- 119	3.14	147.06	H-Bond (Protein Donor)	false
C5N	CB	THR- 155	3.7	0	Hydrophobic	false
C2D	CB	PRO- 157	3.84	0	Hydrophobic	false
C5N	CG	PRO- 157	3.7	0	Hydrophobic	false
O3B	O	VAL- 170	3.2	136.82	H-Bond (Ligand Donor)	false
O3B	N	ASP- 172	2.76	152.71	H-Bond (Protein Donor)	false
O3D	OD2	ASP- 172	2.54	165.68	H-Bond (Ligand Donor)	false
O2D	OD1	ASP- 172	2.59	143.01	H-Bond (Ligand Donor)	false
O2D	OD2	ASP- 172	3.16	151.47	H-Bond (Ligand Donor)	false
C5B	CB	LEU- 173	3.86	0	Hydrophobic	false
O1N	N	ALA- 174	2.73	177.85	H-Bond (Protein Donor)	false
C5N	CB	ALA- 174	4.25	0	Hydrophobic	false
O2N	NZ	LYS- 182	3.74	0	Ionic (Protein Cationic)	false
C1B	CB	PRO- 303	4.19	0	Hydrophobic	false
O2B	N	GLY- 304	2.96	131.48	H-Bond (Protein Donor)	false
O2B	OE2	GLU- 307	2.91	156.61	H-Bond (Ligand Donor)	false
O2B	OE1	GLU- 307	3.47	146.14	H-Bond (Ligand Donor)	false
N7N	O	HOH- 414	2.99	142.51	H-Bond (Ligand Donor)	false