scPDB - 4hmx entry

Protein Data Bank Entry:

PDB ID : 4hmx

Resolution :1.590 Å

Experimental Method : X-ray

Deposition Date : 2012-10-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pyridoxamine 5'-phosphate oxidase
ID:	Q396C5_BURL3
AC:	Q396C5
Organism:	Burkholderia lata
Reign:	Bacteria
TaxID:	482957
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	61 %
B	39 %

Ligand binding site composition:

B-Factor:	15.669
Number of residues:	38
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.171	654.750

% Hydrophobic	% Polar
34.02	65.98
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	65.07 %
Polar Surface area:	217.05 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-31.0193	17.0536	5.17939

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
O3P	CZ	ARG- 63	3.23	0	Ionic (Protein Cationic)	false
O3P	NE	ARG- 63	2.8	146.95	H-Bond (Protein Donor)	false
O3P	NH1	ARG- 63	2.81	144.06	H-Bond (Protein Donor)	false
C2'	CG	ARG- 63	3.75	0	Hydrophobic	false
C8M	CB	VAL- 64	4.07	0	Hydrophobic	false
C9	CB	VAL- 64	4.11	0	Hydrophobic	false
C7	CG1	VAL- 64	3.54	0	Hydrophobic	false
O2'	O	VAL- 64	2.6	162.96	H-Bond (Ligand Donor)	false
N5	N	ALA- 66	3.14	167.4	H-Bond (Protein Donor)	false
C6	CB	ALA- 66	3.91	0	Hydrophobic	false
N3	O	CYS- 78	2.84	166.62	H-Bond (Ligand Donor)	false
O2	OG1	THR- 79	2.76	164.9	H-Bond (Protein Donor)	false
O4'	NZ	LYS- 85	2.82	143.73	H-Bond (Protein Donor)	false
O1P	N	LYS- 85	2.82	169.78	H-Bond (Protein Donor)	false
O1P	NZ	LYS- 85	2.77	157.31	H-Bond (Protein Donor)	false
O1P	NZ	LYS- 85	2.77	0	Ionic (Protein Cationic)	false
C7M	CZ	TYR- 100	3.87	0	Hydrophobic	false
C8M	CE1	TYR- 100	3.78	0	Hydrophobic	false
O2'	NE2	GLN- 107	2.89	170.8	H-Bond (Protein Donor)	false
O2	NE2	GLN- 142	3.11	153.28	H-Bond (Protein Donor)	false
C5'	CG	GLN- 142	3.88	0	Hydrophobic	false
C8M	CH2	TRP- 185	3.32	0	Hydrophobic	false
O2P	NH2	ARG- 195	2.89	167.91	H-Bond (Protein Donor)	false
O2P	CZ	ARG- 195	3.78	0	Ionic (Protein Cationic)	false
O3'	O	HOH- 402	2.89	146.95	H-Bond (Protein Donor)	false
O2P	O	HOH- 403	2.79	167.84	H-Bond (Protein Donor)	false