scPDB - 1qp8 entry

Protein Data Bank Entry:

PDB ID : 1qp8

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 1999-06-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2-hydroxyacid dehydrogenase
ID:	Q8ZXP5_PYRAE
AC:	Q8ZXP5
Organism:	Pyrobaculum aerophilum
Reign:	Archaea
TaxID:	178306
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	57.791
Number of residues:	53
Including
Standard Amino Acids:	52
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.782	587.250

% Hydrophobic	% Polar
40.23	59.77
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	64.15 %
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
37.2365	-0.0603333	99.9694

Binding mode :

What is Poseview ?

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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
C5D	CB	ALA- 59	4.26	0	Hydrophobic	false
C3D	CB	ALA- 59	4.19	0	Hydrophobic	false
C5N	CB	ALA- 59	3.72	0	Hydrophobic	false
C4N	CG2	VAL- 86	3.93	0	Hydrophobic	false
O3B	N	LEU- 132	3.17	123.13	H-Bond (Protein Donor)	false
O1N	N	ILE- 135	2.82	155.42	H-Bond (Protein Donor)	false
C5D	CD1	ILE- 135	4.46	0	Hydrophobic	false
O3B	OG	SER- 154	3.05	159.08	H-Bond (Ligand Donor)	false
N3A	N	ARG- 155	3.17	129.53	H-Bond (Protein Donor)	false
O2X	NH2	ARG- 155	3.39	134.91	H-Bond (Protein Donor)	false
O2X	CZ	ARG- 155	3.99	0	Ionic (Protein Cationic)	false
O1X	OG1	THR- 156	2.62	158.59	H-Bond (Protein Donor)	false
O1X	N	THR- 156	3.02	141.65	H-Bond (Protein Donor)	false
O3X	OG1	THR- 156	3.24	129.83	H-Bond (Protein Donor)	false
C1B	CG	PRO- 183	4.4	0	Hydrophobic	false
C3D	CB	PRO- 183	4.47	0	Hydrophobic	false
C5B	CG	PRO- 183	4.01	0	Hydrophobic	false
C4D	CG	PRO- 183	4.18	0	Hydrophobic	false
N6A	OD1	ASN- 185	3.08	162.87	H-Bond (Ligand Donor)	false
N7N	OD1	ASP- 235	3.4	151.84	H-Bond (Ligand Donor)	false