scPDB - 4dpm entry

Protein Data Bank Entry:

PDB ID : 4dpm

Resolution :2.300 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
E	100 %

Ligand binding site composition:

B-Factor:	72.346
Number of residues:	55
Including
Standard Amino Acids:	51
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.434	1279.125

% Hydrophobic	% Polar
45.65	54.35
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	57.88 %
Polar Surface area:	426.11 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
7.8634	-19.9203	51.6622

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
O5A	N	LEU- 18	2.92	143.72	H-Bond (Protein Donor)	false
CDP	CG2	VAL- 19	3.49	0	Hydrophobic	false
C2P	CG2	VAL- 19	3.92	0	Hydrophobic	false
C1B	CB	LYS- 41	4.35	0	Hydrophobic	false
O9A	N	LYS- 41	3.05	140.93	H-Bond (Protein Donor)	false
O2B	N	GLY- 42	2.86	151.8	H-Bond (Protein Donor)	false
O7A	OG	SER- 43	2.67	132.27	H-Bond (Protein Donor)	false
O8A	OG	SER- 43	3.47	135.56	H-Bond (Protein Donor)	false
O9A	N	SER- 43	2.76	151.17	H-Bond (Protein Donor)	false
O9A	OG	SER- 43	3.38	155.6	H-Bond (Protein Donor)	false
N8P	O	PRO- 86	3.23	164.63	H-Bond (Ligand Donor)	false
C2P	SG	CYS- 153	3.86	0	Hydrophobic	false
S1P	CB	CYS- 153	3.71	0	Hydrophobic	false
O4A	N	TYR- 187	2.84	171.69	H-Bond (Protein Donor)	false
S1P	CB	ASN- 335	4.29	0	Hydrophobic	false
S1P	CG2	THR- 336	4.31	0	Hydrophobic	false
O1A	MG	MG- 401	2.06	0	Metal Acceptor	false
O4A	MG	MG- 401	2.51	0	Metal Acceptor	false
N3A	O	HOH- 602	3.22	179.96	H-Bond (Protein Donor)	false
O3B	O	HOH- 633	3.38	180	H-Bond (Protein Donor)	false