scPDB - 5bqf entry

Protein Data Bank Entry:

PDB ID : 5bqf

Resolution :1.450 Å

Experimental Method : X-ray

Deposition Date : 2015-05-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Probable hydroxyacid dehydrogenase protein
ID:	Q2KDT2_RHIEC
AC:	Q2KDT2
Organism:	Rhizobium etli
Reign:	Bacteria
TaxID:	347834
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	13.714
Number of residues:	53
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.724	1026.000

% Hydrophobic	% Polar
44.08	55.92
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	66.72 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
28.6734	-7.53412	-3.39929

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
C5N	CB	ALA- 74	3.55	0	Hydrophobic	false
O2A	NH1	ARG- 92	3.04	120.18	H-Bond (Protein Donor)	false
C5N	CD2	LEU- 98	3.76	0	Hydrophobic	false
C3N	CE	MET- 102	3.45	0	Hydrophobic	false
O3B	N	LEU- 147	2.86	148.75	H-Bond (Protein Donor)	false
O2A	N	ILE- 149	3.03	162.73	H-Bond (Protein Donor)	false
O2N	N	LEU- 150	2.85	158.84	H-Bond (Protein Donor)	false
C5N	CD1	LEU- 150	3.82	0	Hydrophobic	false
C5D	CD1	LEU- 150	4.15	0	Hydrophobic	false
C2B	CB	SER- 169	4.44	0	Hydrophobic	false
O2B	N	ARG- 170	3.32	164.95	H-Bond (Protein Donor)	false
O2X	N	THR- 171	2.82	170.39	H-Bond (Protein Donor)	false
C1B	CD2	LEU- 200	3.88	0	Hydrophobic	false
C5B	CG	PRO- 201	4.13	0	Hydrophobic	false
N7N	O	ALA- 232	2.91	157.76	H-Bond (Ligand Donor)	false
N7N	OD2	ASP- 258	2.95	173.54	H-Bond (Ligand Donor)	false
O7N	N	ALA- 285	3.17	134.17	H-Bond (Protein Donor)	false
C4N	CB	ALA- 285	4.09	0	Hydrophobic	false
C5B	CE2	TYR- 319	4.33	0	Hydrophobic	false
C2B	CE2	TYR- 319	3.76	0	Hydrophobic	false
O2B	OH	TYR- 319	3.44	121.75	H-Bond (Protein Donor)	false
O3X	OH	TYR- 319	2.57	174.33	H-Bond (Protein Donor)	false
O2N	O	HOH- 526	2.67	159.87	H-Bond (Protein Donor)	false
O2D	O	HOH- 652	2.83	167.59	H-Bond (Protein Donor)	false