scPDB - 4h2w entry

Protein Data Bank Entry:

PDB ID : 4h2w

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:	Amino acid--[acyl-carrier-protein] ligase 1
ID:	AACL1_BRADU
AC:	Q89VT8
Organism:	Bradyrhizobium diazoefficiens
Reign:	Bacteria
TaxID:	224911
EC Number:	6.2.1.n2

Chains:

Chain Name:	Percentage of Residues within binding site
A	97 %
D	3 %

Ligand binding site composition:

B-Factor:	21.920
Number of residues:	35
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	CL ZN

Cavity properties

Ligandability	Volume (Å3)
0.755	1269.000

% Hydrophobic	% Polar
39.63	60.37
According to VolSite

Ligand :

HET Code:	5GP
Formula:	C10H12N5O8P
Molecular weight:	361.205 g/mol
DrugBank ID:	-
Buried Surface Area:	65.54 %
Polar Surface area:	217.22 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
-3.39333	-2.39083	22.4395

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
O6	N	LEU- 169	3.48	120.07	H-Bond (Protein Donor)	false
N1	N	LEU- 169	2.99	168.89	H-Bond (Protein Donor)	false
C1'	CE2	PHE- 172	4.45	0	Hydrophobic	false
C1'	SD	MET- 174	3.66	0	Hydrophobic	false
C4'	CE	MET- 174	3.4	0	Hydrophobic	false
O3P	NZ	LYS- 235	2.56	161.28	H-Bond (Protein Donor)	false
O3P	NZ	LYS- 235	2.56	0	Ionic (Protein Cationic)	false
O3P	OG	SER- 253	3.38	158.81	H-Bond (Protein Donor)	false
C5'	CB	ALA- 281	4	0	Hydrophobic	false
DuAr	CZ	ARG- 286	3.8	164.29	Pi/Cation	false
C2'	CD	ARG- 286	3.45	0	Hydrophobic	false