scPDB - 4ros entry

Protein Data Bank Entry:

PDB ID : 4ros

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2014-10-28

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_METEP
AC:	A9W386
Organism:	Methylobacterium extorquens
Reign:	Bacteria
TaxID:	419610
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	36.533
Number of residues:	40
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.614	384.750

% Hydrophobic	% Polar
45.61	54.39
According to VolSite

Ligand :

HET Code:	APR
Formula:	C15H21N5O14P2
Molecular weight:	557.300 g/mol
DrugBank ID:	-
Buried Surface Area:	61.14 %
Polar Surface area:	316.8 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	4
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
18.4934	-20.4099	-6.94778

Binding mode :

What is Poseview ?

2D View
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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	GLN- 13	2.88	171.59	H-Bond (Protein Donor)	false
O1B	N	ILE- 14	2.94	171.92	H-Bond (Protein Donor)	false
C5D	CD1	ILE- 14	4.26	0	Hydrophobic	false
C1D	CD1	ILE- 14	4.1	0	Hydrophobic	false
O2'	OD2	ASP- 34	3.39	135.73	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 34	2.66	166.25	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 34	2.67	175.08	H-Bond (Ligand Donor)	false
C5D	CB	THR- 78	4	0	Hydrophobic	false
O4'	N	GLY- 80	3.24	145.17	H-Bond (Protein Donor)	false
O3D	O	VAL- 81	2.93	146.83	H-Bond (Ligand Donor)	false
C2D	CB	PRO- 82	4.15	0	Hydrophobic	false
C1D	CG2	ILE- 119	4.04	0	Hydrophobic	false
O2D	ND2	ASN- 121	2.71	169.41	H-Bond (Protein Donor)	false
O3D	N	ASN- 121	3.12	172.89	H-Bond (Protein Donor)	false
C2D	CB	ASN- 121	4.38	0	Hydrophobic	false
O1B	O	HOH- 510	2.79	179.95	H-Bond (Protein Donor)	false