scPDB - 4gi5 entry

Protein Data Bank Entry:

PDB ID : 4gi5

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2012-08-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative NAD(P)H dehydrogenase (Quinone)
ID:	A6THR9_KLEP7
AC:	A6THR9
Organism:	Klebsiella pneumoniae subsp. pneumoniae
Reign:	Bacteria
TaxID:	272620
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	71 %
B	29 %

Ligand binding site composition:

B-Factor:	17.141
Number of residues:	52
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.584	1056.375

% Hydrophobic	% Polar
38.66	61.34
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	71.75 %
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
87.4826	35.4693	73.4715

Binding mode :

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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
O2P	NE2	HIS- 9	2.79	153.76	H-Bond (Protein Donor)	false
O1A	N	LEU- 15	3.14	161.97	H-Bond (Protein Donor)	false
C5B	CB	LEU- 15	4.01	0	Hydrophobic	false
O5'	ND2	ASN- 16	3.4	123.93	H-Bond (Protein Donor)	false
O1P	ND2	ASN- 16	2.82	171.62	H-Bond (Protein Donor)	false
O1P	N	ASN- 16	2.82	157.66	H-Bond (Protein Donor)	false
C8M	CE2	TYR- 48	4.47	0	Hydrophobic	false
C2B	CZ	PHE- 61	4.15	0	Hydrophobic	false
O2A	NE	ARG- 63	2.86	162.14	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 63	3.69	0	Ionic (Protein Cationic)	false
C8M	CB	PRO- 64	3.43	0	Hydrophobic	false
C8M	CG2	THR- 65	3.82	0	Hydrophobic	false
C4'	CB	PRO- 99	3.79	0	Hydrophobic	false
O2'	O	LEU- 100	2.74	165.52	H-Bond (Ligand Donor)	false
C7M	CD2	TRP- 101	4.14	0	Hydrophobic	false
C8M	CE2	TRP- 101	4.1	0	Hydrophobic	false
C6	CB	TRP- 101	3.76	0	Hydrophobic	false
N5	N	TRP- 102	2.89	169.16	H-Bond (Protein Donor)	false
O4	N	PHE- 103	2.86	138.71	H-Bond (Protein Donor)	false
C4'	CB	THR- 152	4.39	0	Hydrophobic	false
O4'	OG1	THR- 152	2.85	148.15	H-Bond (Protein Donor)	false
N1	N	GLY- 154	3.02	153.24	H-Bond (Protein Donor)	false
O2'	N	GLY- 154	3.43	120.32	H-Bond (Protein Donor)	false
O2	N	GLY- 155	2.81	158.83	H-Bond (Protein Donor)	false
O2	OH	TYR- 160	2.56	162.63	H-Bond (Protein Donor)	false
N3	OH	TYR- 160	2.82	134.07	H-Bond (Ligand Donor)	false
O4'	OG1	THR- 197	3.04	140	H-Bond (Protein Donor)	false
C5'	CB	THR- 197	4.29	0	Hydrophobic	false
O3B	O	ASP- 198	3.38	162.15	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 198	2.57	148.63	H-Bond (Ligand Donor)	false
C4B	CB	THR- 200	4.23	0	Hydrophobic	false
C1B	CB	THR- 200	4.09	0	Hydrophobic	false