scPDB - 1p3d entry

Protein Data Bank Entry:

PDB ID : 1p3d

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2003-04-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-N-acetylmuramate--L-alanine ligase
ID:	MURC_HAEIN
AC:	P45066
Organism:	Haemophilus influenzae
Reign:	Bacteria
TaxID:	71421
EC Number:	6.3.2.8

Chains:

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

Ligand binding site composition:

B-Factor:	10.867
Number of residues:	58
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	3
Water Molecules:	8
Cofactors:	ANP
Metals:	MN MN

Cavity properties

Ligandability	Volume (Å3)
0.142	816.750

% Hydrophobic	% Polar
27.69	72.31
According to VolSite

Ligand :

HET Code:	UMA
Formula:	C23H33N4O20P2
Molecular weight:	747.470 g/mol
DrugBank ID:	DB01673
Buried Surface Area:	67.79 %
Polar Surface area:	383.92 Å2

Number of
H-Bond Acceptors:	20
H-Bond Donors:	7
Rings:	3
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
-20.7506	80.0516	64.9315

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
O1A	N	ALA- 29	2.76	157.33	H-Bond (Protein Donor)	false
O1B	N	GLY- 30	2.89	129.67	H-Bond (Protein Donor)	false
O1B	N	MET- 31	2.79	170.64	H-Bond (Protein Donor)	false
O2'	OD2	ASP- 49	2.53	155.17	H-Bond (Ligand Donor)	false
O3B	OD1	ASP- 49	2.73	149.91	H-Bond (Ligand Donor)	false
O3B	OD2	ASP- 49	3.23	146.09	H-Bond (Ligand Donor)	false
O2	N	ILE- 50	3.12	153.25	H-Bond (Protein Donor)	false
C2B	CG1	ILE- 50	4.24	0	Hydrophobic	false
N3	NE2	HIS- 70	2.76	164.06	H-Bond (Ligand Donor)	false
O3A	OG	SER- 84	3.35	131	H-Bond (Protein Donor)	false
O2B	OG	SER- 84	2.73	163.06	H-Bond (Protein Donor)	false
C8'	CB	SER- 85	4.26	0	Hydrophobic	false
C8'	CB	ALA- 86	3.78	0	Hydrophobic	false
C5B	CB	ALA- 86	3.72	0	Hydrophobic	false
C1'	CD	ARG- 107	3.97	0	Hydrophobic	false
C6'	CG	GLU- 173	4.21	0	Hydrophobic	false
C20	CB	SER- 177	3.59	0	Hydrophobic	false
C23	CE1	TYR- 346	4.24	0	Hydrophobic	false
O19	NE	ARG- 377	2.83	160.6	H-Bond (Protein Donor)	false
O20	NE	ARG- 377	3.37	140.5	H-Bond (Protein Donor)	false
O20	NH2	ARG- 377	2.96	161.63	H-Bond (Protein Donor)	false
O19	CZ	ARG- 377	3.78	0	Ionic (Protein Cationic)	false
O20	CZ	ARG- 377	3.61	0	Ionic (Protein Cationic)	false
O19	NH2	ARG- 380	3.18	133.41	H-Bond (Protein Donor)	false
O19	NH1	ARG- 380	2.72	159.74	H-Bond (Protein Donor)	false
O19	CZ	ARG- 380	3.38	0	Ionic (Protein Cationic)	false
C23	CB	ALA- 459	3.71	0	Hydrophobic	false
O6'	O	HOH- 621	2.74	179.96	H-Bond (Protein Donor)	false
O4	O	HOH- 1080	2.75	179.95	H-Bond (Protein Donor)	false
O18	MN	MN- 1604	2.16	0	Metal Acceptor	false