scPDB - 4hjf entry

Protein Data Bank Entry:

PDB ID : 4hjf

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2012-10-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	GGDEF family protein
ID:	Q9A310_CAUCR
AC:	Q9A310
Organism:	Caulobacter crescentus
Reign:	Bacteria
TaxID:	190650
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	25.436
Number of residues:	45
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	2
Water Molecules:	5
Cofactors:
Metals:	CA CA

Cavity properties

Ligandability	Volume (Å3)
0.381	769.500

% Hydrophobic	% Polar
42.11	57.89
According to VolSite

Ligand :

HET Code:	C2E
Formula:	C20H22N10O14P2
Molecular weight:	688.395 g/mol
DrugBank ID:	-
Buried Surface Area:	60.13 %
Polar Surface area:	366.32 Å2

Number of
H-Bond Acceptors:	20
H-Bond Donors:	6
Rings:	7
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
-17.7194	21.6874	-13.6124

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
N71	NE2	GLN- 309	3.21	164.51	H-Bond (Protein Donor)	false
C3'	CD2	LEU- 325	4.45	0	Hydrophobic	false
C5A	CD2	LEU- 325	4.46	0	Hydrophobic	false
C2A	CD1	LEU- 325	3.91	0	Hydrophobic	false
N7	N	ALA- 326	3	170.22	H-Bond (Protein Donor)	false
O1P	NH2	ARG- 327	2.95	137.38	H-Bond (Protein Donor)	false
O1P	NH1	ARG- 327	2.72	151.17	H-Bond (Protein Donor)	false
C5'	CG	PRO- 338	4.14	0	Hydrophobic	false
C1'	CB	PRO- 338	4.45	0	Hydrophobic	false
C1'	CD1	LEU- 342	3.44	0	Hydrophobic	false
N2	OG	SER- 386	3.4	158.54	H-Bond (Ligand Donor)	false
C1A	CD	ARG- 470	4.35	0	Hydrophobic	false
N11	OE2	GLU- 506	2.61	167.6	H-Bond (Ligand Donor)	false
N21	OE2	GLU- 506	3.44	125.8	H-Bond (Ligand Donor)	false
O61	N	PHE- 525	2.8	173.02	H-Bond (Protein Donor)	false
O11	CA	CA- 601	2.18	0	Metal Acceptor	false
O21	CA	CA- 602	2.35	0	Metal Acceptor	false
O6	O	HOH- 710	2.73	143.86	H-Bond (Protein Donor)	false
O2P	O	HOH- 733	2.66	165.09	H-Bond (Protein Donor)	false
O21	O	HOH- 829	2.9	179.99	H-Bond (Protein Donor)	false