scPDB - 1ikg entry

Protein Data Bank Entry:

PDB ID : 1ikg

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2001-05-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	D-alanyl-D-alanine carboxypeptidase
ID:	DAC_STRSR
AC:	P15555
Organism:	Streptomyces sp.
Reign:	Bacteria
TaxID:	31952
EC Number:	3.4.16.4

Chains:

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

Ligand binding site composition:

B-Factor:	6.991
Number of residues:	42
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.761	546.750

% Hydrophobic	% Polar
36.42	63.58
According to VolSite

Ligand :

HET Code:	REX
Formula:	C15H25N4O7
Molecular weight:	373.382 g/mol
DrugBank ID:	DB02578
Buried Surface Area:	67.72 %
Polar Surface area:	195.19 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	4
Rings:	0
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
20.1953	-13.6036	38.4056

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
C8	CB	SER- 62	4.14	0	Hydrophobic	false
O2	N	SER- 62	2.72	152.33	H-Bond (Protein Donor)	false
N4	O	PHE- 120	2.59	148.19	H-Bond (Ligand Donor)	false
C2	CD2	PHE- 120	3.49	0	Hydrophobic	false
N4	OG1	THR- 123	2.84	165.02	H-Bond (Ligand Donor)	false
N2	OH	TYR- 159	3.19	125.12	H-Bond (Ligand Donor)	false
O1	ND2	ASN- 161	2.79	169.56	H-Bond (Protein Donor)	false
C8	CH2	TRP- 233	4.13	0	Hydrophobic	false
C1	CH2	TRP- 233	3.58	0	Hydrophobic	false
C8	CB	ALA- 234	4.49	0	Hydrophobic	false
O3	CZ	ARG- 285	3.9	0	Ionic (Protein Cationic)	false
O4	CZ	ARG- 285	3.55	0	Ionic (Protein Cationic)	false
O3	NH2	ARG- 285	2.93	165.67	H-Bond (Protein Donor)	false
O4	NE	ARG- 285	2.88	162.09	H-Bond (Protein Donor)	false
O4	NH2	ARG- 285	3.35	134.11	H-Bond (Protein Donor)	false
O4	OG1	THR- 299	2.78	136.48	H-Bond (Protein Donor)	false
C3	CG2	THR- 301	4.18	0	Hydrophobic	false
C4	CG2	THR- 301	3.86	0	Hydrophobic	false
C11	CB	THR- 301	3.98	0	Hydrophobic	false
N1	O	THR- 301	2.88	147.66	H-Bond (Ligand Donor)	false
O2	N	THR- 301	2.79	169.36	H-Bond (Protein Donor)	false
O6	OG	SER- 326	2.54	162.99	H-Bond (Protein Donor)	false
O5	O	HOH- 1067	2.96	179.97	H-Bond (Protein Donor)	false