scPDB - 4kqq entry

Protein Data Bank Entry:

PDB ID : 4kqq

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2013-05-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Peptidoglycan D,D-transpeptidase FtsI
ID:	G3XD46_PSEAE
AC:	G3XD46
Organism:	Pseudomonas aeruginosa
Reign:	Bacteria
TaxID:	208964
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	23.126
Number of residues:	41
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.074	1056.375

% Hydrophobic	% Polar
40.26	59.74
According to VolSite

Ligand :

HET Code:	VPP
Formula:	C23H28N5O8S
Molecular weight:	534.562 g/mol
DrugBank ID:	-
Buried Surface Area:	60.42 %
Polar Surface area:	220.98 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	3
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-2.51324	7.62657	23.1457

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
O01	OG	SER- 294	2.86	124	H-Bond (Protein Donor)	false
O01	NZ	LYS- 297	3.57	0	Ionic (Protein Cationic)	false
C03	CG2	VAL- 333	3.8	0	Hydrophobic	false
S	CG2	VAL- 333	3.32	0	Hydrophobic	false
C08	CG1	VAL- 333	3.74	0	Hydrophobic	false
S	CB	SER- 349	4.11	0	Hydrophobic	false
C02	CB	SER- 349	3.7	0	Hydrophobic	false
O01	OG	SER- 349	2.5	154.88	H-Bond (Protein Donor)	false
O06	ND2	ASN- 351	3.14	158.55	H-Bond (Protein Donor)	false
C	CG2	THR- 404	3.62	0	Hydrophobic	false
O	OH	TYR- 407	3.05	162.82	H-Bond (Protein Donor)	false
C	CB	TYR- 409	3.8	0	Hydrophobic	false
O02	OG	SER- 485	2.55	161.38	H-Bond (Protein Donor)	false
O03	OG	SER- 485	3.21	123.74	H-Bond (Protein Donor)	false
O02	OG1	THR- 487	3.29	136.58	H-Bond (Protein Donor)	false
O07	N	THR- 487	3.15	161.26	H-Bond (Protein Donor)	false
N02	OG1	THR- 487	3.04	141.96	H-Bond (Ligand Donor)	false
N03	O	THR- 487	3.01	126.47	H-Bond (Ligand Donor)	false
C07	CG2	THR- 487	3.86	0	Hydrophobic	false
O04	N	ARG- 489	2.86	168.92	H-Bond (Protein Donor)	false
C07	CG	ARG- 489	4.32	0	Hydrophobic	false
C	CE2	TYR- 498	4.3	0	Hydrophobic	false
C12	CE1	TYR- 503	3.32	0	Hydrophobic	false
C03	CD2	PHE- 533	4.44	0	Hydrophobic	false
O03	N	GLY- 535	2.82	166.71	H-Bond (Protein Donor)	false