scPDB - 2qd5 entry

Protein Data Bank Entry:

PDB ID : 2qd5

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2007-06-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ferrochelatase, mitochondrial
ID:	HEMH_HUMAN
AC:	P22830
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	4.99.1.1

Chains:

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

Ligand binding site composition:

B-Factor:	59.842
Number of residues:	23
Including
Standard Amino Acids:	21
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.448	1360.125

% Hydrophobic	% Polar
59.31	40.69
According to VolSite

Ligand :

HET Code:	CHD
Formula:	C24H39O5
Molecular weight:	407.563 g/mol
DrugBank ID:	DB02659
Buried Surface Area:	38.28 %
Polar Surface area:	100.82 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	4
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
7.88776	20.8013	9.77083

Binding mode :

What is Poseview ?

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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
C18	CE2	PHE- 93	4	0	Hydrophobic	false
C20	CE2	PHE- 93	4.27	0	Hydrophobic	false
C18	SD	MET- 99	3.53	0	Hydrophobic	false
C19	CG	MET- 99	4.28	0	Hydrophobic	false
C15	CD2	LEU- 101	4.18	0	Hydrophobic	false
C7	CD2	LEU- 101	3.72	0	Hydrophobic	false
O25	CZ	ARG- 115	3.75	0	Ionic (Protein Cationic)	false
O25	NH2	ARG- 115	3.27	127.59	H-Bond (Protein Donor)	false
O26	NH2	ARG- 115	3.03	162.14	H-Bond (Protein Donor)	false
C1	CG	PRO- 266	4.02	0	Hydrophobic	false
C2	CB	PRO- 266	3.64	0	Hydrophobic	false
C3	CB	SER- 268	4.33	0	Hydrophobic	false
O3	OG	SER- 268	3.13	172.04	H-Bond (Protein Donor)	false
O12	O	VAL- 305	3.36	171.36	H-Bond (Ligand Donor)	false
C21	CG2	VAL- 305	3.31	0	Hydrophobic	false
C3	SD	MET- 308	3.61	0	Hydrophobic	false
C11	CE	MET- 308	3.56	0	Hydrophobic	false
C2	CE	MET- 308	3.45	0	Hydrophobic	false