scPDB - 4hmz entry

Protein Data Bank Entry:

PDB ID : 4hmz

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2012-10-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	dTDP-4-dehydro-6-deoxyglucose 3-epimerase
ID:	CHMJ_STRBI
AC:	Q5SFD1
Organism:	Streptomyces bikiniensis
Reign:	Bacteria
TaxID:	1896
EC Number:	5.1.3.27

Chains:

Chain Name:	Percentage of Residues within binding site
A	21 %
B	73 %
C	6 %

Ligand binding site composition:

B-Factor:	17.163
Number of residues:	36
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.339	732.375

% Hydrophobic	% Polar
36.41	63.59
According to VolSite

Ligand :

HET Code:	18T
Formula:	C16H24N2O15P2
Molecular weight:	546.314 g/mol
DrugBank ID:	-
Buried Surface Area:	58.3 %
Polar Surface area:	276.36 Å2

Number of
H-Bond Acceptors:	15
H-Bond Donors:	5
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
39.7169	-14.5829	22.1989

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
C4,	CB	HIS- 17	3.86	0	Hydrophobic	false
O1P	CZ	ARG- 21	3.66	0	Ionic (Protein Cationic)	false
O3P	CZ	ARG- 21	3.87	0	Ionic (Protein Cationic)	false
O1P	NH2	ARG- 21	2.72	158.14	H-Bond (Protein Donor)	false
O3P	NH1	ARG- 21	2.93	156.98	H-Bond (Protein Donor)	false
N31	OE2	GLU- 26	2.65	168.84	H-Bond (Ligand Donor)	false
O41	NE2	GLN- 45	2.82	128.5	H-Bond (Protein Donor)	false
O41	ND2	ASN- 47	3.35	124.82	H-Bond (Protein Donor)	false
C5	CB	ARG- 57	4.31	0	Hydrophobic	false
C6	CD	ARG- 57	4.16	0	Hydrophobic	false
O4P	CZ	ARG- 57	3.71	0	Ionic (Protein Cationic)	false
O4P	NH1	ARG- 57	2.69	151.25	H-Bond (Protein Donor)	false
C3	CB	HIS- 60	4.46	0	Hydrophobic	false
O3	NZ	LYS- 70	2.89	132.14	H-Bond (Protein Donor)	false
O4	NH1	ARG- 117	3.07	153.37	H-Bond (Protein Donor)	false
C6	CD2	LEU- 128	3.69	0	Hydrophobic	false
C2	CZ	TYR- 130	4.42	0	Hydrophobic	false
C6	CE1	TYR- 130	4.03	0	Hydrophobic	false
C4	CZ	TYR- 130	3.95	0	Hydrophobic	false
C5A	CE1	TYR- 136	4.04	0	Hydrophobic	false
C2,	CZ	TYR- 136	4.37	0	Hydrophobic	false
O2	OE1	GLU- 141	3.01	147.62	H-Bond (Ligand Donor)	false
O3	OE2	GLU- 141	2.71	148.4	H-Bond (Ligand Donor)	false
O1P	O	HOH- 494	3.33	167.44	H-Bond (Protein Donor)	false