scPDB - 5j23 entry

Protein Data Bank Entry:

PDB ID : 5j23

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2016-03-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative 2-hydroxyacid dehydrogenase
ID:	Q92LZ4_RHIME
AC:	Q92LZ4
Organism:	Rhizobium meliloti
Reign:	Bacteria
TaxID:	266834
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	53.396
Number of residues:	39
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.842	1056.375

% Hydrophobic	% Polar
34.50	65.50
According to VolSite

Ligand :

HET Code:	A2R
Formula:	C15H20N5O17P3
Molecular weight:	635.264 g/mol
DrugBank ID:	-
Buried Surface Area:	62.31 %
Polar Surface area:	378.8 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	4
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
8.47593	67.6858	96.6607

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
C12'	CG1	VAL- 72	3.79	0	Hydrophobic	false
O3'	N	LEU- 150	2.93	154.87	H-Bond (Protein Donor)	false
O2	CZ	ARG- 152	3.49	0	Ionic (Protein Cationic)	false
O2	N	ARG- 152	3.47	165.49	H-Bond (Protein Donor)	false
O11	NH1	ARG- 152	3	159.48	H-Bond (Protein Donor)	false
O12	N	ILE- 153	3.05	163.37	H-Bond (Protein Donor)	false
C1'	CG2	THR- 172	4.26	0	Hydrophobic	false
OP3	NH2	ARG- 173	3.31	133.63	H-Bond (Protein Donor)	false
OP3	NE	ARG- 173	2.78	169.56	H-Bond (Protein Donor)	false
OP3	N	ARG- 173	3.2	158.79	H-Bond (Protein Donor)	false
OP2	NH2	ARG- 173	3.11	141.98	H-Bond (Protein Donor)	false
OP3	CZ	ARG- 173	3.49	0	Ionic (Protein Cationic)	false
OP2	CZ	ARG- 173	3.96	0	Ionic (Protein Cationic)	false
C11'	CD1	ILE- 200	4.29	0	Hydrophobic	false
C14'	CD1	ILE- 200	4.4	0	Hydrophobic	false
C1'	CG1	VAL- 201	4.16	0	Hydrophobic	false
C5'	CG	PRO- 202	4.03	0	Hydrophobic	false
C15'	CG	PRO- 202	4.43	0	Hydrophobic	false
N6	OG	SER- 206	3.08	146.56	H-Bond (Ligand Donor)	false
O11	O	HOH- 556	3.11	179.99	H-Bond (Protein Donor)	false