scPDB - 3o9p entry

Protein Data Bank Entry:

PDB ID : 3o9p

Resolution :2.070 Å

Experimental Method : X-ray

Deposition Date : 2010-08-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Periplasmic murein peptide-binding protein
ID:	MPPA_ECOLI
AC:	P77348
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	24.772
Number of residues:	46
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.098	317.250

% Hydrophobic	% Polar
46.81	53.19
According to VolSite

Ligand :

HET Code:	MHI
Formula:	C15H25N4O8
Molecular weight:	389.381 g/mol
DrugBank ID:	-
Buried Surface Area:	66.9 %
Polar Surface area:	233.86 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	4
Rings:	0
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
13.3196	61.3438	39.4536

Binding mode :

What is Poseview ?

2D View
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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
O5	NZ	LYS- 20	2.78	148.53	H-Bond (Protein Donor)	false
O5	NZ	LYS- 20	2.78	0	Ionic (Protein Cationic)	false
O7	NZ	LYS- 20	3.35	0	Ionic (Protein Cationic)	false
N2	O	VAL- 32	3.17	155.73	H-Bond (Ligand Donor)	false
O4	N	LEU- 34	2.95	165.95	H-Bond (Protein Donor)	false
C7	CG	LEU- 34	4.48	0	Hydrophobic	false
C11	CD1	LEU- 34	3.9	0	Hydrophobic	false
C1	CD1	ILE- 37	3.55	0	Hydrophobic	false
C1	CZ	PHE- 109	4.28	0	Hydrophobic	false
N4	OE1	GLN- 267	2.66	144.57	H-Bond (Ligand Donor)	false
C6	CH2	TRP- 395	4.04	0	Hydrophobic	false
O2	NH2	ARG- 402	3.03	169.86	H-Bond (Protein Donor)	false
O3	NH2	ARG- 402	3.47	125.83	H-Bond (Protein Donor)	false
O3	NH1	ARG- 402	2.65	171.73	H-Bond (Protein Donor)	false
O2	CZ	ARG- 402	3.84	0	Ionic (Protein Cationic)	false
O3	CZ	ARG- 402	3.49	0	Ionic (Protein Cationic)	false
O6	NH2	ARG- 411	2.9	165.18	H-Bond (Protein Donor)	false
O6	NH1	ARG- 411	3.4	135.91	H-Bond (Protein Donor)	false
O6	CZ	ARG- 411	3.6	0	Ionic (Protein Cationic)	false
N3	OG	SER- 413	2.82	137.96	H-Bond (Ligand Donor)	false
O6	OG	SER- 413	2.73	152.8	H-Bond (Protein Donor)	false
C1	CG2	VAL- 415	4.02	0	Hydrophobic	false
C7	CG2	VAL- 415	3.91	0	Hydrophobic	false
C11	CG1	VAL- 415	3.84	0	Hydrophobic	false
N1	O	VAL- 415	2.76	149.4	H-Bond (Ligand Donor)	false
O1	N	VAL- 415	2.97	154.83	H-Bond (Protein Donor)	false
N1	OD2	ASP- 417	3.31	130.15	H-Bond (Ligand Donor)	false
N1	OD1	ASP- 417	2.7	153.8	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 417	3.31	0	Ionic (Ligand Cationic)	false
N1	OD1	ASP- 417	2.7	0	Ionic (Ligand Cationic)	false
C11	CZ	TYR- 483	4.24	0	Hydrophobic	false
C13	CE2	TYR- 483	3.64	0	Hydrophobic	false
N4	O	THR- 484	3.3	149.8	H-Bond (Ligand Donor)	false
O3	O	HOH- 559	2.84	174.02	H-Bond (Protein Donor)	false
N4	O	HOH- 624	2.71	165.59	H-Bond (Ligand Donor)	false