scPDB - 4cr8 entry

Protein Data Bank Entry:

PDB ID : 4cr8

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2014-02-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	N-acylmannosamine 1-dehydrogenase
ID:	DHMA_FLAS1
AC:	P22441
Organism:	Flavobacterium sp.
Reign:	Bacteria
TaxID:	240
EC Number:	1.1.1.233

Chains:

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

Ligand binding site composition:

B-Factor:	11.095
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.369	1309.500

% Hydrophobic	% Polar
44.59	55.41
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	58.83 %
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
-9.15378	-69.8026	97.3393

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
O1A	N	GLY- 26	3.41	170.1	H-Bond (Protein Donor)	false
O1N	N	ILE- 27	3	166.43	H-Bond (Protein Donor)	false
O3B	OD2	ASP- 46	2.81	160.59	H-Bond (Ligand Donor)	false
O3B	OD1	ASP- 46	3.44	140.48	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 46	2.72	159.75	H-Bond (Ligand Donor)	false
O3B	NE	ARG- 50	3.41	120.4	H-Bond (Protein Donor)	false
O3B	NH2	ARG- 50	2.71	133.64	H-Bond (Protein Donor)	false
N6A	OD1	ASP- 67	3.21	154.38	H-Bond (Ligand Donor)	false
N1A	N	LEU- 68	2.88	175.34	H-Bond (Protein Donor)	false
O4B	N	ALA- 96	2.98	173.05	H-Bond (Protein Donor)	false
O5B	O	HOH- 2004	3.3	156.75	H-Bond (Protein Donor)	false