scPDB - 4gap entry

Protein Data Bank Entry:

PDB ID : 4gap

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2012-07-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial
ID:	NDI1_YEAST
AC:	P32340
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	1.6.5.9

Chains:

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

Ligand binding site composition:

B-Factor:	46.532
Number of residues:	55
Including
Standard Amino Acids:	54
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	NAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.359	621.000

% Hydrophobic	% Polar
48.91	51.09
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	73.42 %
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
18.6412	-18.6024	-18.8026

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
O3B	OG	SER- 61	2.93	163.68	H-Bond (Protein Donor)	false
O3B	N	SER- 61	3	141.35	H-Bond (Protein Donor)	false
O1A	N	TRP- 63	3.16	158.22	H-Bond (Protein Donor)	false
C4'	CB	TRP- 63	4.48	0	Hydrophobic	false
O1P	N	GLY- 64	2.91	151.12	H-Bond (Protein Donor)	false
C9	CB	THR- 91	3.9	0	Hydrophobic	false
C7M	CB	LEU- 94	3.92	0	Hydrophobic	false
C7M	CG	PRO- 95	4.05	0	Hydrophobic	false
N6A	O	ALA- 129	2.94	160.91	H-Bond (Ligand Donor)	false
N1A	N	ALA- 129	3.01	163.96	H-Bond (Protein Donor)	false
C7M	CG	LEU- 195	4.4	0	Hydrophobic	false
C8M	CD	LYS- 196	4.35	0	Hydrophobic	false
C7M	CG2	THR- 239	3.58	0	Hydrophobic	false
O3'	OD2	ASP- 383	3.29	143.62	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 383	3.28	156.91	H-Bond (Ligand Donor)	false
C5'	CB	ASP- 383	4.35	0	Hydrophobic	false
O2P	N	ASP- 383	2.83	152.62	H-Bond (Protein Donor)	false
N1	N	ALA- 393	3.38	169.92	H-Bond (Protein Donor)	false
O2	N	ALA- 393	3.45	121.9	H-Bond (Protein Donor)	false
C2'	CB	ALA- 393	3.81	0	Hydrophobic	false
C5'	CB	ALA- 396	4.23	0	Hydrophobic	false
N3	O7N	NAD- 602	3.39	140.01	H-Bond (Ligand Donor)	false
C9A	C5D	NAD- 602	4.39	0	Hydrophobic	false
C1'	C4D	NAD- 602	4.26	0	Hydrophobic	false