scPDB - 4wji entry

Protein Data Bank Entry:

PDB ID : 4wji

Resolution :1.400 Å

Experimental Method : X-ray

Deposition Date : 2014-09-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase
ID:	Q92MG1_RHIME
AC:	Q92MG1
Organism:	Rhizobium meliloti
Reign:	Bacteria
TaxID:	266834
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	11.953
Number of residues:	55
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.148	722.250

% Hydrophobic	% Polar
47.66	52.34
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	65.62 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
28.3055	0.198458	4.42942

Binding mode :

What is Poseview ?

2D View
3D View

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
O3B	N	ILE- 13	3.02	168.38	H-Bond (Protein Donor)	false
O1A	N	LEU- 15	2.85	164.45	H-Bond (Protein Donor)	false
O2N	N	ILE- 16	2.92	168.81	H-Bond (Protein Donor)	false
C3N	CG1	ILE- 16	3.72	0	Hydrophobic	false
C4N	CD1	ILE- 16	3.63	0	Hydrophobic	false
O3B	OG1	THR- 37	2.74	150.72	H-Bond (Ligand Donor)	false
O2X	OG1	THR- 37	2.84	158.28	H-Bond (Protein Donor)	false
O3X	NE	ARG- 38	2.83	171.81	H-Bond (Protein Donor)	false
O3X	NH2	ARG- 38	3.47	132.36	H-Bond (Protein Donor)	false
O3X	CZ	ARG- 38	3.6	0	Ionic (Protein Cationic)	false
O2X	N	SER- 39	2.91	153.74	H-Bond (Protein Donor)	false
O2X	OG	SER- 39	2.77	153.97	H-Bond (Protein Donor)	false
O1X	OG1	THR- 42	2.75	175.22	H-Bond (Protein Donor)	false
C5D	CB	SER- 72	4.48	0	Hydrophobic	false
C1B	CG1	VAL- 73	4.14	0	Hydrophobic	false
O3D	O	VAL- 73	2.72	154.36	H-Bond (Ligand Donor)	false
C4D	CG2	VAL- 98	3.97	0	Hydrophobic	false
C2D	CB	SER- 100	4.44	0	Hydrophobic	false
O2D	N	SER- 100	3.41	140.55	H-Bond (Protein Donor)	false
C5N	CG	PRO- 124	4.36	0	Hydrophobic	false
O1A	N	GLY- 132	2.86	173.93	H-Bond (Protein Donor)	false
C2D	SD	MET- 235	3.86	0	Hydrophobic	false
C3N	CE	MET- 235	3.62	0	Hydrophobic	false
O7N	N	TYR- 302	2.82	146.92	H-Bond (Protein Donor)	false
C4N	CE2	TYR- 302	3.35	0	Hydrophobic	false
O2N	O	HOH- 547	2.71	168.15	H-Bond (Protein Donor)	false
O2D	O	HOH- 549	2.99	161.34	H-Bond (Ligand Donor)	false
N7N	O	HOH- 632	2.91	168.86	H-Bond (Ligand Donor)	false