scPDB - 3gvh entry

Protein Data Bank Entry:

PDB ID : 3gvh

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2009-03-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Malate dehydrogenase
ID:	MDH_BRUA2
AC:	Q2YLR9
Organism:	Brucella abortus
Reign:	Bacteria
TaxID:	359391
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	26.727
Number of residues:	41
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.717	594.000

% Hydrophobic	% Polar
36.36	63.64
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	52.48 %
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
-57.4292	-8.40195	38.3763

Binding mode :

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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	MET- 13	3.39	151.04	H-Bond (Protein Donor)	false
O1N	N	ILE- 14	3.36	156.3	H-Bond (Protein Donor)	false
C5N	CD1	ILE- 14	4.35	0	Hydrophobic	false
C5D	CD1	ILE- 14	4.14	0	Hydrophobic	false
O3B	OD2	ASP- 34	2.66	172.02	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 34	2.94	173.31	H-Bond (Ligand Donor)	false
C5D	CB	THR- 78	4.14	0	Hydrophobic	false
C3N	CG2	ILE- 119	3.92	0	Hydrophobic	false
N7N	O	ILE- 119	2.93	142.88	H-Bond (Ligand Donor)	false
O2D	ND2	ASN- 121	2.52	148.96	H-Bond (Protein Donor)	false
C4N	CD2	LEU- 148	3.78	0	Hydrophobic	false
O7N	NE2	HIS- 176	2.6	148.69	H-Bond (Protein Donor)	false
C5N	CG	PRO- 235	3.98	0	Hydrophobic	false
O5B	O	HOH- 378	3.45	143.46	H-Bond (Protein Donor)	false