scPDB - 4gh5 entry

Protein Data Bank Entry:

PDB ID : 4gh5

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2012-08-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Short-chain dehydrogenase/reductase SDR
ID:	A7IQH5_XANP2
AC:	A7IQH5
Organism:	Xanthobacter autotrophicus
Reign:	Bacteria
TaxID:	78245
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	11.534
Number of residues:	53
Including
Standard Amino Acids:	51
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.470	1167.750

% Hydrophobic	% Polar
56.65	43.35
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	75.15 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
10.3416	46.6204	21.9929

Binding mode :

What is Poseview ?

2D View
3D View

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
O1N	N	ILE- 19	2.85	161.34	H-Bond (Protein Donor)	false
C3N	CD1	ILE- 19	4.42	0	Hydrophobic	false
C5D	CD1	ILE- 19	4.07	0	Hydrophobic	false
O3B	OD2	ASP- 38	2.7	165.63	H-Bond (Ligand Donor)	false
O3B	OD1	ASP- 38	3.4	123.1	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 38	2.63	155.07	H-Bond (Ligand Donor)	false
N3A	N	LEU- 39	3.13	144.74	H-Bond (Protein Donor)	false
N6A	OD1	ASP- 64	2.95	151.16	H-Bond (Ligand Donor)	false
N1A	N	VAL- 65	3.09	168.75	H-Bond (Protein Donor)	false
O3D	O	ASN- 91	2.82	129.74	H-Bond (Ligand Donor)	false
C4D	CD2	PHE- 141	3.55	0	Hydrophobic	false
C5N	CB	SER- 143	3.84	0	Hydrophobic	false
O2D	OH	TYR- 156	2.81	158.25	H-Bond (Ligand Donor)	false
O3D	NZ	LYS- 160	2.91	145.07	H-Bond (Protein Donor)	false
C5N	CB	PRO- 186	3.52	0	Hydrophobic	false
O7N	N	VAL- 189	2.85	169.96	H-Bond (Protein Donor)	false
N7N	O	VAL- 189	3.27	130.78	H-Bond (Ligand Donor)	false
O1A	N	MET- 194	3.24	159.86	H-Bond (Protein Donor)	false
C3N	SD	MET- 194	4.31	0	Hydrophobic	false
C2D	CE	MET- 194	3.57	0	Hydrophobic	false
O1N	O	HOH- 411	2.66	179.99	H-Bond (Protein Donor)	false