scPDB - 2cvz entry

Protein Data Bank Entry:

PDB ID : 2cvz

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2005-06-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	3-hydroxyisobutyrate dehydrogenase
ID:	Q5SLQ6_THET8
AC:	Q5SLQ6
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	300852
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	22.936
Number of residues:	46
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.013	664.875

% Hydrophobic	% Polar
45.18	54.82
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	65.02 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
32.4269	-33.9611	9.59929

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- 11	2.85	173.61	H-Bond (Protein Donor)	false
O2N	N	MET- 12	2.92	161.08	H-Bond (Protein Donor)	false
C3N	CG	MET- 12	3.45	0	Hydrophobic	false
C4N	SD	MET- 12	3.76	0	Hydrophobic	false
C5N	CE	MET- 12	4.09	0	Hydrophobic	false
O3B	OD1	ASN- 30	2.76	134.94	H-Bond (Ligand Donor)	false
O2X	ND2	ASN- 30	2.96	164.95	H-Bond (Protein Donor)	false
O1X	NE	ARG- 31	2.99	177.45	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 31	2.87	170.57	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 31	3.78	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 31	3.81	0	Ionic (Protein Cationic)	false
O1X	OG1	THR- 32	2.7	157.31	H-Bond (Protein Donor)	false
O1X	N	THR- 32	3.02	127.41	H-Bond (Protein Donor)	false
C4D	SG	CYS- 62	3.79	0	Hydrophobic	false
C1B	CD2	LEU- 63	3.84	0	Hydrophobic	false
O3D	O	LEU- 63	3.05	150.09	H-Bond (Ligand Donor)	false
C5B	CG	PRO- 64	3.89	0	Hydrophobic	false
N6A	OE2	GLU- 71	3.01	151.65	H-Bond (Ligand Donor)	false
O3D	N	SER- 91	3.07	164.74	H-Bond (Protein Donor)	false
C2D	CB	SER- 91	4.4	0	Hydrophobic	false
C5N	CG2	VAL- 116	4.25	0	Hydrophobic	false
N7N	O	THR- 226	2.88	177.27	H-Bond (Ligand Donor)	false
C2D	CE1	PHE- 227	4.06	0	Hydrophobic	false
C2D	CD1	LEU- 231	3.89	0	Hydrophobic	false
O3D	NZ	LYS- 234	3.2	132.01	H-Bond (Protein Donor)	false
O2D	NZ	LYS- 234	3.06	143.15	H-Bond (Protein Donor)	false
O2N	O	HOH- 1333	2.68	150.68	H-Bond (Protein Donor)	false
O2D	O	HOH- 1343	2.7	160.22	H-Bond (Ligand Donor)	false