scPDB - 2yvw entry

Protein Data Bank Entry:

PDB ID : 2yvw

Resolution :1.810 Å

Experimental Method : X-ray

Deposition Date : 2007-04-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-N-acetylglucosamine 1-carboxyvinyltransferase
ID:	MURA_AQUAE
AC:	O67315
Organism:	Aquifex aeolicus
Reign:	Bacteria
TaxID:	224324
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	18.474
Number of residues:	50
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.923	1110.375

% Hydrophobic	% Polar
41.03	58.97
According to VolSite

Ligand :

HET Code:	EPU
Formula:	C20H26N3O19P2
Molecular weight:	674.377 g/mol
DrugBank ID:	-
Buried Surface Area:	61.24 %
Polar Surface area:	354.82 Å2

Number of
H-Bond Acceptors:	19
H-Bond Donors:	6
Rings:	3
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
95.8894	43.6711	7.19184

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
O1E	NZ	LYS- 31	3.51	0	Ionic (Protein Cationic)	false
O2E	NZ	LYS- 31	2.51	0	Ionic (Protein Cationic)	false
O2E	NZ	LYS- 31	2.51	160.84	H-Bond (Protein Donor)	false
C8	CB	ASN- 32	4.48	0	Hydrophobic	false
O3	ND2	ASN- 32	3.32	124.37	H-Bond (Protein Donor)	false
O2E	ND2	ASN- 32	3.24	156.88	H-Bond (Protein Donor)	false
C8	CD2	LEU- 35	3.92	0	Hydrophobic	false
C8	CB	ALA- 101	3.65	0	Hydrophobic	false
O2B	NH2	ARG- 129	3.17	170.47	H-Bond (Protein Donor)	false
N3U	OD1	ASP- 132	2.68	170.54	H-Bond (Ligand Donor)	false
O4U	N	GLN- 133	2.76	148.88	H-Bond (Protein Donor)	false
C1D	CD1	LEU- 168	4.14	0	Hydrophobic	false
O1A	OG1	THR- 170	2.68	168.73	H-Bond (Protein Donor)	false
O2A	N	VAL- 171	2.91	161.73	H-Bond (Protein Donor)	false
C1	CB	VAL- 171	3.82	0	Hydrophobic	false
C6	CG2	VAL- 171	4.39	0	Hydrophobic	false
O1B	OG1	THR- 172	2.83	160.6	H-Bond (Protein Donor)	false
O1B	N	THR- 172	2.79	167.43	H-Bond (Protein Donor)	false
C1	CG2	THR- 172	4.42	0	Hydrophobic	false
C8	CG2	THR- 172	4.01	0	Hydrophobic	false
C6	CG2	THR- 310	3.79	0	Hydrophobic	false
O4	OD2	ASP- 311	3.08	144.84	H-Bond (Ligand Donor)	false
O4	OD1	ASP- 311	2.8	150.54	H-Bond (Ligand Donor)	false
O3D	O	ILE- 333	2.63	153.92	H-Bond (Ligand Donor)	false
C6	CG2	ILE- 333	4.14	0	Hydrophobic	false
C5D	CG2	ILE- 333	3.9	0	Hydrophobic	false
C5D	CE1	PHE- 334	4.44	0	Hydrophobic	false
C3D	CE1	PHE- 334	3.57	0	Hydrophobic	false
C5	CE2	PHE- 334	3.76	0	Hydrophobic	false
O2E	O	HOH- 639	2.76	179.96	H-Bond (Protein Donor)	false