scPDB - 4yag entry

Protein Data Bank Entry:

PDB ID : 4yag

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2015-02-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	C alpha-dehydrogenase
ID:	C0SUJ9_9SPHN
AC:	C0SUJ9
Organism:	Sphingobium sp. SYK-6
Reign:	Bacteria
TaxID:	627192
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	14.542
Number of residues:	56
Including
Standard Amino Acids:	53
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.094	762.750

% Hydrophobic	% Polar
45.58	54.42
According to VolSite

Ligand :

HET Code:	NAI
Formula:	C21H27N7O14P2
Molecular weight:	663.425 g/mol
DrugBank ID:	DB00157
Buried Surface Area:	83.71 %
Polar Surface area:	342.9 Å2

Number of
H-Bond Acceptors:	19
H-Bond Donors:	6
Rings:	5
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
45.9485	56.3903	12.7753

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
O2A	OG	SER- 15	2.7	151.97	H-Bond (Protein Donor)	false
C3B	CB	SER- 15	3.94	0	Hydrophobic	false
O1N	N	ILE- 17	2.75	153.64	H-Bond (Protein Donor)	false
C5D	CB	ILE- 17	4.27	0	Hydrophobic	false
C4D	CD1	ILE- 17	4.43	0	Hydrophobic	false
C1D	CD1	ILE- 17	4.42	0	Hydrophobic	false
O3B	OD2	ASP- 36	2.66	168.38	H-Bond (Ligand Donor)	false
O3B	OD1	ASP- 36	3.2	127.06	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 36	2.69	160.89	H-Bond (Ligand Donor)	false
N3A	N	ILE- 37	3.21	133.24	H-Bond (Protein Donor)	false
N6A	OD1	ASP- 64	2.99	162.64	H-Bond (Ligand Donor)	false
N1A	N	VAL- 65	3.06	163.68	H-Bond (Protein Donor)	false
O3D	O	ASN- 91	2.85	143.38	H-Bond (Ligand Donor)	false
C1B	CB	ALA- 92	4.42	0	Hydrophobic	false
C1D	CG2	THR- 142	3.8	0	Hydrophobic	false
C4D	CG2	THR- 142	3.73	0	Hydrophobic	false
O2D	OH	TYR- 158	2.82	160.01	H-Bond (Ligand Donor)	false
O3D	NZ	LYS- 162	2.9	142.07	H-Bond (Protein Donor)	false
O2D	NZ	LYS- 162	3	136.2	H-Bond (Protein Donor)	false
C4N	CB	PRO- 188	3.89	0	Hydrophobic	false
O7N	N	ILE- 191	2.97	170.77	H-Bond (Protein Donor)	false
N7N	O	ILE- 191	3.03	146.58	H-Bond (Ligand Donor)	false
O2N	OG	SER- 193	2.68	155.87	H-Bond (Protein Donor)	false
O2A	N	ARG- 194	2.77	158.66	H-Bond (Protein Donor)	false
C2D	CD1	ILE- 195	3.61	0	Hydrophobic	false
O5B	O	HOH- 710	2.95	162.54	H-Bond (Protein Donor)	false
O1A	O	HOH- 716	2.65	179.98	H-Bond (Protein Donor)	false