scPDB - 4udr entry

Protein Data Bank Entry:

PDB ID : 4udr

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2014-12-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	5-(hydroxymethyl)furfural oxidase
ID:	HMFO_METS6
AC:	E4QP00
Organism:	Methylovorus sp.
Reign:	Bacteria
TaxID:	887061
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	7.584
Number of residues:	66
Including
Standard Amino Acids:	62
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.873	702.000

% Hydrophobic	% Polar
42.79	57.21
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	77.52 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
35.5582	13.9866	39.3447

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	THR- 15	3.14	168.87	H-Bond (Protein Donor)	false
O1A	OG1	THR- 15	3.5	123.01	H-Bond (Protein Donor)	false
O4'	OG1	THR- 15	3.05	161.06	H-Bond (Protein Donor)	false
C4'	CB	THR- 15	4.25	0	Hydrophobic	false
O2P	N	ALA- 16	2.95	165.79	H-Bond (Protein Donor)	false
O3B	OE1	GLU- 36	2.74	169.33	H-Bond (Ligand Donor)	false
O2B	OE2	GLU- 36	2.6	164.13	H-Bond (Ligand Donor)	false
O2B	OE1	GLU- 36	3.49	135.35	H-Bond (Ligand Donor)	false
N3A	N	ALA- 37	3.07	141.86	H-Bond (Protein Donor)	false
C7M	CD	ARG- 60	3.71	0	Hydrophobic	false
O2B	NE1	TRP- 68	3.23	135.73	H-Bond (Protein Donor)	false
C2B	CZ2	TRP- 68	4.03	0	Hydrophobic	false
C7M	CB	GLU- 90	4.23	0	Hydrophobic	false
C8M	CB	GLU- 90	4.37	0	Hydrophobic	false
O1A	N	GLY- 98	2.77	170.29	H-Bond (Protein Donor)	false
C8M	CG2	VAL- 101	4.25	0	Hydrophobic	false
O2'	ND2	ASN- 102	3.25	155.91	H-Bond (Protein Donor)	false
C9A	CB	ASN- 102	3.45	0	Hydrophobic	false
N5	N	MET- 103	3.06	175.2	H-Bond (Protein Donor)	false
C6	CG	MET- 103	4.34	0	Hydrophobic	false
N3	O	VAL- 105	2.87	145.95	H-Bond (Ligand Donor)	false
O4	N	VAL- 105	3.13	156.07	H-Bond (Protein Donor)	false
N6A	O	VAL- 233	2.91	161.72	H-Bond (Ligand Donor)	false
N1A	N	VAL- 233	2.99	152.9	H-Bond (Protein Donor)	false
C7M	CD2	TRP- 466	3.74	0	Hydrophobic	false
C6	CE3	TRP- 466	3.45	0	Hydrophobic	false
C8	CB	TRP- 466	3.27	0	Hydrophobic	false
C5'	CB	ALA- 501	4.34	0	Hydrophobic	false
O1P	N	ALA- 501	3.17	169.46	H-Bond (Protein Donor)	false
O3'	OG1	THR- 512	2.7	167.77	H-Bond (Protein Donor)	false
N1	N	ASN- 513	3.31	134.34	H-Bond (Protein Donor)	false
O2	N	ASN- 513	2.75	145.09	H-Bond (Protein Donor)	false
O2'	ND2	ASN- 513	3.11	128.44	H-Bond (Protein Donor)	false
O4'	ND2	ASN- 513	3.07	121.35	H-Bond (Protein Donor)	false
C2'	CB	ASN- 513	3.79	0	Hydrophobic	false
C5'	CG2	THR- 516	4.2	0	Hydrophobic	false
O2P	O	HOH- 2007	2.82	171.94	H-Bond (Protein Donor)	false
O2	O	HOH- 2131	2.66	179.97	H-Bond (Protein Donor)	false