scPDB - 5dld entry

Protein Data Bank Entry:

PDB ID : 5dld

Resolution :1.450 Å

Experimental Method : X-ray

Deposition Date : 2015-09-04

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 2-epimerase
ID:	A4JLG9_BURVG
AC:	A4JLG9
Organism:	Burkholderia vietnamiensis )
Reign:	Bacteria
TaxID:	269482
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	11.307
Number of residues:	43
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.791	786.375

% Hydrophobic	% Polar
46.35	53.65
According to VolSite

Ligand :

HET Code:	UD1
Formula:	C17H25N3O17P2
Molecular weight:	605.338 g/mol
DrugBank ID:	DB03397
Buried Surface Area:	79.46 %
Polar Surface area:	325.69 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	7
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
17.3899	-9.81318	-1.44413

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
C1'	CG2	THR- 10	4.43	0	Hydrophobic	false
C4'	CG	PRO- 12	4.27	0	Hydrophobic	false
C6'	CG	PRO- 12	3.58	0	Hydrophobic	false
O7'	NE2	GLN- 39	2.95	169.32	H-Bond (Protein Donor)	false
O1A	NE2	GLN- 39	2.86	160.25	H-Bond (Protein Donor)	false
O1B	NE2	HIS- 40	2.79	147.93	H-Bond (Protein Donor)	false
O4	N	ARG- 41	3.04	141.28	H-Bond (Protein Donor)	false
O4	N	MET- 43	2.93	168.79	H-Bond (Protein Donor)	false
C2B	SD	MET- 62	4	0	Hydrophobic	false
C3B	CG	MET- 62	4.2	0	Hydrophobic	false
O3B	O	ARG- 63	2.62	151.31	H-Bond (Ligand Donor)	false
O2'	N	GLY- 65	2.93	172.83	H-Bond (Protein Donor)	false
C3B	CG	GLN- 66	4.2	0	Hydrophobic	false
C5B	CG	GLN- 66	4.31	0	Hydrophobic	false
O3B	N	GLN- 66	2.98	164.26	H-Bond (Protein Donor)	false
O5B	NE2	GLN- 66	3.45	130.75	H-Bond (Protein Donor)	false
O2A	NE2	GLN- 66	3.24	165.81	H-Bond (Protein Donor)	false
C8'	CD2	LEU- 68	3.42	0	Hydrophobic	false
C3'	CG2	THR- 97	4.47	0	Hydrophobic	false
C8'	CB	THR- 98	4.15	0	Hydrophobic	false
O7'	N	THR- 98	2.82	165.3	H-Bond (Protein Donor)	false
C8'	CG	PRO- 131	3.6	0	Hydrophobic	false
O3'	OE2	GLU- 132	2.62	158.17	H-Bond (Ligand Donor)	false
O4'	NE2	HIS- 214	2.94	163.98	H-Bond (Protein Donor)	false
O4'	NH1	ARG- 215	2.92	160.2	H-Bond (Protein Donor)	false
O1B	NE2	HIS- 247	2.96	161.11	H-Bond (Protein Donor)	false
C1B	CB	LEU- 248	4.26	0	Hydrophobic	false
O2B	ND2	ASN- 249	2.78	165.55	H-Bond (Protein Donor)	false
O2A	O	HOH- 678	2.7	179.96	H-Bond (Protein Donor)	false
N2'	O	HOH- 743	2.89	155.91	H-Bond (Ligand Donor)	false