scPDB - 4rgq entry

Protein Data Bank Entry:

PDB ID : 4rgq

Resolution :2.230 Å

Experimental Method : X-ray

Deposition Date : 2014-09-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glycerol-1-phosphate dehydrogenase [NAD(P)+]
ID:	G1PDH_METJA
AC:	Q58122
Organism:	Methanocaldococcus jannaschii
Reign:	Archaea
TaxID:	243232
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	36.035
Number of residues:	51
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.587	837.000

% Hydrophobic	% Polar
38.71	61.29
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	60.32 %
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
-20.9222	51.9582	75.51

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	ND2	ASN- 38	3.06	149.94	H-Bond (Protein Donor)	false
O2X	N	ASN- 38	2.75	128.67	H-Bond (Protein Donor)	false
O2X	OG1	THR- 39	3.44	173.83	H-Bond (Protein Donor)	false
O2X	N	THR- 39	3.28	123.4	H-Bond (Protein Donor)	false
O1X	OH	TYR- 52	3.29	134.22	H-Bond (Protein Donor)	false
O3X	OH	TYR- 52	2.85	156.79	H-Bond (Protein Donor)	false
O1N	N	GLY- 78	3.04	157.24	H-Bond (Protein Donor)	false
O2A	N	ARG- 79	2.82	151.06	H-Bond (Protein Donor)	false
O3D	NH1	ARG- 79	2.76	131.37	H-Bond (Protein Donor)	false
C2D	CB	ASP- 82	4.48	0	Hydrophobic	false
O2D	OD2	ASP- 82	3.05	165.4	H-Bond (Ligand Donor)	false
N7A	OG1	THR- 100	3.04	160.09	H-Bond (Protein Donor)	false
N6A	O	THR- 100	2.98	156.96	H-Bond (Ligand Donor)	false
O1N	OG	SER- 103	2.66	139.71	H-Bond (Protein Donor)	false
O5D	ND2	ASN- 104	3.16	121.9	H-Bond (Protein Donor)	false
O4D	ND2	ASN- 104	3.26	148.19	H-Bond (Protein Donor)	false
C5N	CB	ASN- 104	4.11	0	Hydrophobic	false
N7N	OG	SER- 109	2.83	142.11	H-Bond (Ligand Donor)	false
C2D	CB	SER- 113	4.13	0	Hydrophobic	false
C3N	CB	SER- 113	3.9	0	Hydrophobic	false
O7N	OG	SER- 113	2.76	175.72	H-Bond (Protein Donor)	false
C1B	CD1	LEU- 141	4.2	0	Hydrophobic	false
C5B	CD2	LEU- 141	3.87	0	Hydrophobic	false
C5D	CB	HIS- 247	4.39	0	Hydrophobic	false
O3X	O	HOH- 520	2.54	168.31	H-Bond (Protein Donor)	false