scPDB - 4h38 entry

Protein Data Bank Entry:

PDB ID : 4h38

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2012-09-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)
ID:	UPPS_ECOLI
AC:	P60472
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	2.5.1.31

Chains:

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

Ligand binding site composition:

B-Factor:	29.559
Number of residues:	26
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.550	695.250

% Hydrophobic	% Polar
64.56	35.44
According to VolSite

Ligand :

HET Code:	0YX
Formula:	C21H26BrO5P
Molecular weight:	469.306 g/mol
DrugBank ID:	-
Buried Surface Area:	47.78 %
Polar Surface area:	91.46 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	0
Rings:	2
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
44.3476	29.6688	60.8077

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
CAA	CB	HIS- 43	3.78	0	Hydrophobic	false
CAQ	CB	ALA- 47	3.34	0	Hydrophobic	false
CAQ	CB	ALA- 47	3.34	0	Hydrophobic	false
CAS	CB	VAL- 50	4.04	0	Hydrophobic	false
CAF	CG1	VAL- 50	3.41	0	Hydrophobic	false
OAD	CZ	ARG- 51	2.79	0	Ionic (Protein Cationic)	false
CAL	CD	ARG- 51	3.84	0	Hydrophobic	false
CAT	CB	ARG- 51	4.34	0	Hydrophobic	false
CAK	CB	ARG- 51	4.42	0	Hydrophobic	false
CBA	CG	ARG- 51	3.5	0	Hydrophobic	false
CAT	CG2	VAL- 54	4.35	0	Hydrophobic	false
CAG	CG2	VAL- 54	4.42	0	Hydrophobic	false
CAJ	CG1	VAL- 54	3.89	0	Hydrophobic	false
CAR	CE1	PHE- 89	4.11	0	Hydrophobic	false
CAP	CD1	PHE- 89	4.43	0	Hydrophobic	false
CAO	CB	ALA- 92	3.47	0	Hydrophobic	false
CAO	CB	ALA- 92	3.47	0	Hydrophobic	false
CAF	CD1	LEU- 93	3.29	0	Hydrophobic	false
CAG	CB	GLU- 96	4.48	0	Hydrophobic	false
CAK	CG	GLU- 96	3.68	0	Hydrophobic	false
CAY	CG	GLU- 96	3.62	0	Hydrophobic	false
OAB	OG	SER- 99	3.04	150.74	H-Bond (Protein Donor)	false
CAL	CB	SER- 99	4.38	0	Hydrophobic	false
CAG	CD1	LEU- 100	3.94	0	Hydrophobic	false
CAJ	CD2	LEU- 100	3.62	0	Hydrophobic	false
CAT	CD2	LEU- 100	3.6	0	Hydrophobic	false
BRE	CB	HIS- 103	4.15	0	Hydrophobic	false
CAG	CD2	LEU- 139	4.11	0	Hydrophobic	false
CAF	CD1	ILE- 141	3.97	0	Hydrophobic	false