scPDB - 3kpk entry

Protein Data Bank Entry:

PDB ID : 3kpk

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2009-11-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Sulfide-quinone reductase
ID:	SQRD_ACIF2
AC:	B7JBP8
Organism:	Acidithiobacillus ferrooxidans )
Reign:	Bacteria
TaxID:	243159
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	36.537
Number of residues:	64
Including
Standard Amino Acids:	57
Non Standard Amino Acids:	0
Water Molecules:	7
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.122	1593.000

% Hydrophobic	% Polar
57.84	42.16
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	63.97 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
42.5798	-22.823	7.93628

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
O2A	N	THR- 11	3.1	169.04	H-Bond (Protein Donor)	false
O4'	OG1	THR- 11	2.79	173.96	H-Bond (Protein Donor)	false
C4'	CB	THR- 11	3.6	0	Hydrophobic	false
O1P	N	GLY- 12	2.84	170.45	H-Bond (Protein Donor)	false
O3B	OG	SER- 34	3.33	121.6	H-Bond (Ligand Donor)	false
N3A	N	ALA- 35	3.1	133.6	H-Bond (Protein Donor)	false
C3'	CG1	VAL- 42	4.13	0	Hydrophobic	false
C8	CG1	VAL- 42	3.49	0	Hydrophobic	false
C7M	CG	PRO- 46	4.22	0	Hydrophobic	false
N6A	O	ALA- 78	2.96	164.1	H-Bond (Ligand Donor)	false
N1A	N	ALA- 78	2.88	157.02	H-Bond (Protein Donor)	false
C7M	CD1	ILE- 127	3.52	0	Hydrophobic	false
C8M	SG	CYS- 128	3.99	0	Hydrophobic	false
C7M	CB	PRO- 163	3.7	0	Hydrophobic	false
C9A	CG	PRO- 163	4.45	0	Hydrophobic	false
C6	CG	PRO- 163	3.39	0	Hydrophobic	false
C8M	CZ	PHE- 264	4.11	0	Hydrophobic	false
C3'	CD1	ILE- 302	4.45	0	Hydrophobic	false
C5'	CD1	ILE- 302	3.83	0	Hydrophobic	false
O2P	N	ILE- 302	2.83	157.46	H-Bond (Protein Donor)	false
O2	N	GLY- 322	2.68	159.75	H-Bond (Protein Donor)	false
C2'	CD1	ILE- 325	4.11	0	Hydrophobic	false
C5'	CD1	ILE- 325	3.71	0	Hydrophobic	false
O4	NZ	LYS- 391	2.73	126.03	H-Bond (Protein Donor)	false
O2P	O	HOH- 435	2.67	160.69	H-Bond (Protein Donor)	false
O1P	O	HOH- 437	2.76	155.34	H-Bond (Protein Donor)	false