scPDB - 2bwp entry

Protein Data Bank Entry:

PDB ID : 2bwp

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2005-07-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	5-aminolevulinate synthase
ID:	HEM1_RHOCB
AC:	P18079
Organism:	Rhodobacter capsulatus
Reign:	Bacteria
TaxID:	272942
EC Number:	2.3.1.37

Chains:

Chain Name:	Percentage of Residues within binding site
A	77 %
B	23 %

Ligand binding site composition:

B-Factor:	25.846
Number of residues:	39
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.107	982.125

% Hydrophobic	% Polar
48.45	51.55
According to VolSite

Ligand :

HET Code:	PLG
Formula:	C10H13N2O7P
Molecular weight:	304.193 g/mol
DrugBank ID:	DB02824
Buried Surface Area:	80.03 %
Polar Surface area:	172.09 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	2
Rings:	1
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
25.3778	7.2203	11.5466

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
O	ND2	ASN- 54	2.75	137.84	H-Bond (Protein Donor)	false
C5A	CB	ALA- 115	3.92	0	Hydrophobic	false
OP1	N	ALA- 115	3.04	158.59	H-Bond (Protein Donor)	false
C5A	CB	TYR- 116	4.11	0	Hydrophobic	false
OP3	N	TYR- 116	2.8	160.34	H-Bond (Protein Donor)	false
C2A	CB	HIS- 142	3.72	0	Hydrophobic	false
DuAr	DuAr	HIS- 142	3.36	0	Aromatic Face/Face	false
N1	OD2	ASP- 214	2.69	173.28	H-Bond (Ligand Donor)	false
C2A	CB	VAL- 216	4.21	0	Hydrophobic	false
C5	CG1	VAL- 216	3.74	0	Hydrophobic	false
O3	NE2	HIS- 217	2.69	148.94	H-Bond (Protein Donor)	false
OP1	OG1	THR- 245	2.66	144.8	H-Bond (Protein Donor)	false
C4	CE	LYS- 248	4.3	0	Hydrophobic	false
OP2	NZ	LYS- 248	3.45	127.23	H-Bond (Protein Donor)	false
OP3	OG	SER- 277	2.7	150.86	H-Bond (Protein Donor)	false
OP2	N	THR- 278	2.7	159.03	H-Bond (Protein Donor)	false
OP2	OG1	THR- 278	2.6	170.49	H-Bond (Protein Donor)	false