scPDB - 1umk entry

Protein Data Bank Entry:

PDB ID : 1umk

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2003-10-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NADH-cytochrome b5 reductase 3
ID:	NB5R3_HUMAN
AC:	P00387
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.6.2.2

Chains:

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

Ligand binding site composition:

B-Factor:	17.748
Number of residues:	42
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.487	462.375

% Hydrophobic	% Polar
32.85	67.15
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	59.38 %
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
63.0633	47.1286	-5.79828

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
C7M	CB	HIS- 77	4.44	0	Hydrophobic	false
O1A	NH2	ARG- 91	3.32	168.13	H-Bond (Protein Donor)	false
O2A	NE	ARG- 91	3.23	123.3	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 91	3.23	121.96	H-Bond (Protein Donor)	false
O1P	NE	ARG- 91	2.88	139.9	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 91	3.57	0	Ionic (Protein Cationic)	false
O1P	CZ	ARG- 91	3.62	0	Ionic (Protein Cationic)	false
C2'	CB	ARG- 91	4.48	0	Hydrophobic	false
C3'	CD	ARG- 91	4.16	0	Hydrophobic	false
O2'	O	PRO- 92	2.7	175	H-Bond (Ligand Donor)	false
C7	CB	PRO- 92	4.19	0	Hydrophobic	false
C8	CG	PRO- 92	3.62	0	Hydrophobic	false
C2'	CE1	TYR- 93	3.7	0	Hydrophobic	false
C3'	CZ	TYR- 93	4.42	0	Hydrophobic	false
C4'	CE1	TYR- 93	4.39	0	Hydrophobic	false
O4'	OH	TYR- 93	2.77	129.09	H-Bond (Ligand Donor)	false
N5	N	THR- 94	3.37	154.48	H-Bond (Protein Donor)	false
C6	CB	THR- 94	4.37	0	Hydrophobic	false
N3	O	VAL- 108	2.65	174.08	H-Bond (Ligand Donor)	false
O2	N	LYS- 110	2.99	161.42	H-Bond (Protein Donor)	false
C3B	CE1	TYR- 112	4.42	0	Hydrophobic	false
C5'	CE2	TYR- 112	3.78	0	Hydrophobic	false
N6A	O	PHE- 113	2.79	121.13	H-Bond (Ligand Donor)	false
C1B	CG	PHE- 120	3.68	0	Hydrophobic	false
O1A	N	LYS- 125	2.98	177.87	H-Bond (Protein Donor)	false
O1P	N	MET- 126	2.86	153.04	H-Bond (Protein Donor)	false
O2P	N	SER- 127	2.76	157.88	H-Bond (Protein Donor)	false
O2P	OG	SER- 127	2.64	148.82	H-Bond (Protein Donor)	false
C6	CG	PRO- 185	3.81	0	Hydrophobic	false
C7	SG	CYS- 273	4.16	0	Hydrophobic	false
C7M	CB	PHE- 300	4.02	0	Hydrophobic	false