scPDB - 4dpl entry

Protein Data Bank Entry:

PDB ID : 4dpl

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2012-02-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Malonyl-CoA reductase
ID:	MCR_SULTO
AC:	Q96YK1
Organism:	Sulfolobus tokodaii
Reign:	Archaea
TaxID:	273063
EC Number:	1.2.1.75

Chains:

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

Ligand binding site composition:

B-Factor:	32.074
Number of residues:	55
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.309	955.125

% Hydrophobic	% Polar
38.52	61.48
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	62.62 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
56.7609	5.13385	4.34417

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
O3B	OG1	THR- 16	2.8	152.3	H-Bond (Ligand Donor)	false
O2A	N	LEU- 18	3.08	167.1	H-Bond (Protein Donor)	false
O1N	N	VAL- 19	2.92	155.75	H-Bond (Protein Donor)	false
C3N	CG2	VAL- 19	3.66	0	Hydrophobic	false
O2X	N	LYS- 41	3.32	159.92	H-Bond (Protein Donor)	false
O3X	N	GLY- 42	2.75	153.94	H-Bond (Protein Donor)	false
O2X	OG	SER- 43	2.65	151.58	H-Bond (Protein Donor)	false
O2X	N	SER- 43	3.32	135.1	H-Bond (Protein Donor)	false
C4D	CB	PRO- 86	4.11	0	Hydrophobic	false
O3D	O	LEU- 87	2.61	167.59	H-Bond (Ligand Donor)	false
C4N	SG	CYS- 153	3.69	0	Hydrophobic	false
N7N	O	SER- 183	3.13	145.75	H-Bond (Ligand Donor)	false
O1A	N	TYR- 187	3.34	165.5	H-Bond (Protein Donor)	false
O7N	ND2	ASN- 335	2.87	161.23	H-Bond (Protein Donor)	false
C5N	CB	ALA- 340	3.47	0	Hydrophobic	false
O1N	O	HOH- 515	2.75	129.99	H-Bond (Protein Donor)	false
N3A	O	HOH- 628	2.55	179.96	H-Bond (Protein Donor)	false
O3B	O	HOH- 668	3.41	143.03	H-Bond (Protein Donor)	false