scPDB - 5c4n entry

Protein Data Bank Entry:

PDB ID : 5c4n

Resolution :1.630 Å

Experimental Method : X-ray

Deposition Date : 2015-06-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Precorrin-6A reductase
ID:	COBK_RHOCB
AC:	O68098
Organism:	Rhodobacter capsulatus
Reign:	Bacteria
TaxID:	272942
EC Number:	1.3.1.54

Chains:

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

Ligand binding site composition:

B-Factor:	18.555
Number of residues:	43
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.887	945.000

% Hydrophobic	% Polar
41.43	58.57
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	58.38 %
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
11.985	56.1418	-29.2125

Binding mode :

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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
N6A	O	GLY- 8	3.5	124.49	H-Bond (Ligand Donor)	false
N6A	O	SER- 30	3.01	149.91	H-Bond (Ligand Donor)	false
N1A	OG	SER- 30	2.74	158.7	H-Bond (Protein Donor)	false
C1B	CB	ALA- 32	4.41	0	Hydrophobic	false
O3X	N	PHE- 50	2.82	153.1	H-Bond (Protein Donor)	false
O2X	N	GLY- 51	2.86	149.11	H-Bond (Protein Donor)	false
O1X	N	GLY- 52	3.14	132.15	H-Bond (Protein Donor)	false
O2X	N	GLY- 52	3.31	163.38	H-Bond (Protein Donor)	false
O7N	NE2	HIS- 73	3.09	129.07	H-Bond (Protein Donor)	false
C3D	CB	HIS- 73	4.23	0	Hydrophobic	false
C3D	CB	PHE- 75	3.99	0	Hydrophobic	false
C5N	CB	PHE- 75	3.04	0	Hydrophobic	false
C3D	CB	ALA- 76	4.45	0	Hydrophobic	false
C5B	CB	GLN- 78	4.37	0	Hydrophobic	false
C3B	CG	GLN- 78	4.31	0	Hydrophobic	false
O2A	N	MET- 79	2.87	167.32	H-Bond (Protein Donor)	false
C3B	CB	MET- 79	4.24	0	Hydrophobic	false
C2B	SD	MET- 79	3.89	0	Hydrophobic	false
O1N	NE2	GLN- 137	3.2	150.52	H-Bond (Protein Donor)	false
O5D	NE2	GLN- 137	3.3	137.45	H-Bond (Protein Donor)	false
N1N	NZ	LYS- 196	3.24	165.3	H-Bond (Protein Donor)	false
C3N	CG	LYS- 196	3.89	0	Hydrophobic	false
C5N	CG	LYS- 196	3.38	0	Hydrophobic	false
C6N	NZ	LYS- 196	2.74	154.31	Weak HBond PROT	false
DuAr	NZ	LYS- 196	3.27	141.78	Pi/Cation	false
O1A	O	HOH- 443	2.67	179.99	H-Bond (Protein Donor)	false
O3X	O	HOH- 449	2.69	179.97	H-Bond (Protein Donor)	false