scPDB - 3nd1 entry

Protein Data Bank Entry:

PDB ID : 3nd1

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2010-06-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Precorrin-6A synthase (Deacetylating)
ID:	D5AV00_RHOCB
AC:	D5AV00
Organism:	Rhodobacter capsulatus
Reign:	Bacteria
TaxID:	272942
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	13.032
Number of residues:	38
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.682	519.750

% Hydrophobic	% Polar
59.74	40.26
According to VolSite

Ligand :

HET Code:	SAH
Formula:	C14H20N6O5S
Molecular weight:	384.411 g/mol
DrugBank ID:	DB01752
Buried Surface Area:	71.75 %
Polar Surface area:	212.38 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
57.061	69.001	23.7866

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
N6	O	THR- 11	3.07	135.86	H-Bond (Ligand Donor)	false
N	O	ASP- 114	2.96	132.73	H-Bond (Ligand Donor)	false
O	N	ASP- 114	2.88	172.83	H-Bond (Protein Donor)	false
N	O	LEU- 117	2.74	177.75	H-Bond (Ligand Donor)	false
SD	CB	TYR- 118	4.03	0	Hydrophobic	false
OXT	N	ALA- 144	2.87	161.74	H-Bond (Protein Donor)	false
C1'	CB	ALA- 144	3.78	0	Hydrophobic	false
CB	CE	MET- 186	3.67	0	Hydrophobic	false
C4'	CE	MET- 186	4.04	0	Hydrophobic	false
C1'	CE	MET- 186	3.93	0	Hydrophobic	false
C4'	CD2	LEU- 187	4.16	0	Hydrophobic	false
SD	CD2	LEU- 187	3.67	0	Hydrophobic	false
O3'	N	LEU- 187	3.31	123.57	H-Bond (Protein Donor)	false
O2'	N	LEU- 187	3.24	148.56	H-Bond (Protein Donor)	false
N6	O	VAL- 209	2.98	127.54	H-Bond (Ligand Donor)	false
N1	N	VAL- 209	2.94	146.62	H-Bond (Protein Donor)	false
C3'	SD	MET- 243	4.17	0	Hydrophobic	false
C2'	CB	MET- 243	4.44	0	Hydrophobic	false
O2'	O	ASP- 244	2.87	151.52	H-Bond (Ligand Donor)	false
N	O	HOH- 282	2.86	162.83	H-Bond (Ligand Donor)	false
O3'	O	HOH- 354	3.06	179.96	H-Bond (Protein Donor)	false
O2'	O	HOH- 362	3.19	130.92	H-Bond (Ligand Donor)	false