scPDB - 3c1m entry

Protein Data Bank Entry:

PDB ID : 3c1m

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2008-01-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Probable aspartokinase
ID:	AK_METJA
AC:	Q57991
Organism:	Methanocaldococcus jannaschii
Reign:	Archaea
TaxID:	243232
EC Number:	2.7.2.4

Chains:

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

Ligand binding site composition:

B-Factor:	22.942
Number of residues:	45
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.034	408.375

% Hydrophobic	% Polar
41.32	58.68
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	68.85 %
Polar Surface area:	322.68 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-40.1251	15.0533	47.0644

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
O2G	NZ	LYS- 6	2.92	148.73	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 6	2.92	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 6	3.38	0	Ionic (Protein Cationic)	false
O3G	N	GLY- 9	3.08	150.08	H-Bond (Protein Donor)	false
O2G	OG	SER- 40	2.71	160.09	H-Bond (Protein Donor)	false
O1B	OG1	THR- 230	2.86	156.92	H-Bond (Protein Donor)	false
O3A	OG1	THR- 230	3.45	126.16	H-Bond (Protein Donor)	false
O3'	OD1	ASP- 231	2.82	170.94	H-Bond (Ligand Donor)	false
C3'	CG1	VAL- 232	3.83	0	Hydrophobic	false
N6	O	TYR- 236	3.11	149.09	H-Bond (Ligand Donor)	false
N1	N	TYR- 236	2.79	162.63	H-Bond (Protein Donor)	false
O2'	OD1	ASP- 239	2.77	171.47	H-Bond (Ligand Donor)	false
C2'	CG	PRO- 240	4.36	0	Hydrophobic	false
C2'	CD	ARG- 241	4.46	0	Hydrophobic	false
O2A	NZ	LYS- 266	3.6	0	Ionic (Protein Cationic)	false
C1'	CB	LYS- 266	4.16	0	Hydrophobic	false
C5'	CG1	VAL- 267	3.79	0	Hydrophobic	false
O1G	MG	MG- 471	2.12	0	Metal Acceptor	false
O2B	MG	MG- 471	2.17	0	Metal Acceptor	false
O1A	MG	MG- 471	1.99	0	Metal Acceptor	false
O1B	O	HOH- 477	2.77	158.61	H-Bond (Protein Donor)	false