scPDB - 4i4z entry

Protein Data Bank Entry:

PDB ID : 4i4z

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2012-11-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	1,4-dihydroxy-2-naphthoyl-CoA synthase
ID:	P73495_SYNY3
AC:	P73495
Organism:	Synechocystis sp.
Reign:	Bacteria
TaxID:	1111708
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	89 %
F	11 %

Ligand binding site composition:

B-Factor:	39.837
Number of residues:	46
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.018	698.625

% Hydrophobic	% Polar
57.49	42.51
According to VolSite

Ligand :

HET Code:	2NE
Formula:	C28H36N7O18P3S
Molecular weight:	883.608 g/mol
DrugBank ID:	-
Buried Surface Area:	53.82 %
Polar Surface area:	449.91 Å2

Number of
H-Bond Acceptors:	23
H-Bond Donors:	6
Rings:	4
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	21

Mass center Coordinates

X	Y	Z
42.4586	-49.6721	10.7716

Binding mode :

What is Poseview ?

2D View
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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
C17	CD	LYS- 30	4.48	0	Hydrophobic	false
C03	CB	ARG- 31	4.22	0	Hydrophobic	false
C04	CD	ARG- 31	4.04	0	Hydrophobic	false
C14	CG	ARG- 31	4.02	0	Hydrophobic	false
O08	CZ	ARG- 31	3.6	0	Ionic (Protein Cationic)	false
O08	NH1	ARG- 31	3.23	144.79	H-Bond (Protein Donor)	false
O08	NE	ARG- 31	3.09	155.51	H-Bond (Protein Donor)	false
O09	NE	ARG- 31	3.26	121.39	H-Bond (Protein Donor)	false
C03	CB	SER- 75	3.85	0	Hydrophobic	false
C42	CB	SER- 75	4.29	0	Hydrophobic	false
N31	O	SER- 75	3.09	131.7	H-Bond (Ligand Donor)	false
N45	O	SER- 75	3.13	139.12	H-Bond (Ligand Donor)	false
N31	O	GLY- 77	3.06	156.81	H-Bond (Ligand Donor)	false
O50	N	GLY- 77	2.76	166.08	H-Bond (Protein Donor)	false
N32	N	GLN- 79	2.94	163.57	H-Bond (Protein Donor)	false
C47	CG	GLN- 79	4.49	0	Hydrophobic	false
C57	CE1	TYR- 87	3.37	0	Hydrophobic	false
C56	CD2	LEU- 96	4.4	0	Hydrophobic	false
C55	CG1	VAL- 98	3.38	0	Hydrophobic	false
C03	CG	TYR- 119	4.16	0	Hydrophobic	false
C04	CE2	TYR- 119	3.96	0	Hydrophobic	false
C01	CD1	TYR- 119	4	0	Hydrophobic	false
C01	CG1	ILE- 121	4.16	0	Hydrophobic	false
C03	CG1	ILE- 121	4.04	0	Hydrophobic	false
C42	CG2	ILE- 121	3.91	0	Hydrophobic	false
O50	N	GLY- 123	2.64	127.3	H-Bond (Protein Donor)	false
O44	OG1	THR- 145	2.61	145.6	H-Bond (Protein Donor)	false
C47	CG2	VAL- 149	4.17	0	Hydrophobic	false
S48	CB	SER- 151	3.88	0	Hydrophobic	false
C18	CZ	PHE- 260	4.12	0	Hydrophobic	false
O24	NZ	LYS- 263	2.64	161.57	H-Bond (Protein Donor)	false
O24	NZ	LYS- 263	2.64	0	Ionic (Protein Cationic)	false