scPDB - 1hyg entry

Protein Data Bank Entry:

PDB ID : 1hyg

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2001-01-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))
ID:	MDH_METJA
AC:	Q60176
Organism:	Methanocaldococcus jannaschii
Reign:	Archaea
TaxID:	243232
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	98 %
B	2 %

Ligand binding site composition:

B-Factor:	40.071
Number of residues:	51
Including
Standard Amino Acids:	51
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.864	1015.875

% Hydrophobic	% Polar
37.54	62.46
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	54.78 %
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
76.3063	14.2058	35.8137

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
O1X	OG	SER- 9	2.79	151.82	H-Bond (Protein Donor)	false
O1N	N	ARG- 11	3.26	123.1	H-Bond (Protein Donor)	false
O2N	N	VAL- 12	3.24	127.5	H-Bond (Protein Donor)	false
C5D	CG2	VAL- 12	4.16	0	Hydrophobic	false
O2X	N	ARG- 34	2.68	167.09	H-Bond (Protein Donor)	false
O1X	OG	SER- 37	2.58	152.31	H-Bond (Protein Donor)	false
O2X	OG	SER- 37	3.17	125.27	H-Bond (Protein Donor)	false
O3D	O	THR- 81	3.24	158.18	H-Bond (Ligand Donor)	false
C1B	CB	SER- 82	4.18	0	Hydrophobic	false
O4B	N	GLY- 83	3.24	147.39	H-Bond (Protein Donor)	false
C5N	CB	SER- 228	3.46	0	Hydrophobic	false