scPDB - 4y9d entry

Protein Data Bank Entry:

PDB ID : 4y9d

Resolution :2.010 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:	G2IN91_9SPHN
AC:	G2IN91
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:	54.352
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.274	351.000

% Hydrophobic	% Polar
33.65	66.35
According to VolSite

Ligand :

HET Code:	NAI
Formula:	C21H27N7O14P2
Molecular weight:	663.425 g/mol
DrugBank ID:	DB00157
Buried Surface Area:	52.32 %
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
-12.2698	21.6199	-26.7767

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
C3B	CB	SER- 16	4.39	0	Hydrophobic	false
O1N	N	ALA- 18	3.23	149.72	H-Bond (Protein Donor)	false
O3B	OD1	ASP- 37	3.42	123.68	H-Bond (Ligand Donor)	false
O2B	OD2	ASP- 37	3.22	124.99	H-Bond (Ligand Donor)	false
O3B	NH1	ARG- 39	3.06	133.23	H-Bond (Protein Donor)	false
C2B	CD	ARG- 39	4.09	0	Hydrophobic	false
N6A	OD1	ASP- 63	2.91	165.57	H-Bond (Ligand Donor)	false
N1A	N	ILE- 64	3.33	161.69	H-Bond (Protein Donor)	false
C1B	CB	ALA- 92	4.25	0	Hydrophobic	false
O5B	O	HOH- 509	3.34	156.47	H-Bond (Protein Donor)	false