scPDB - 4j1t entry

Protein Data Bank Entry:

PDB ID : 4j1t

Resolution :2.370 Å

Experimental Method : X-ray

Deposition Date : 2013-02-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NAD/NADP transhydrogenase alpha subunit 1
ID:	Q72GR8_THET2
AC:	Q72GR8
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	262724
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	38.713
Number of residues:	31
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.073	1522.125

% Hydrophobic	% Polar
45.68	54.32
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	41.04 %
Polar Surface area:	343.54 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
-19.8806	8.50466	-66.9492

Binding mode :

What is Poseview ?

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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
O2N	NH1	ARG- 122	3.14	169.74	H-Bond (Protein Donor)	false
C3D	CG	ARG- 122	4.13	0	Hydrophobic	false
C2D	CB	ARG- 122	4.27	0	Hydrophobic	false
O1N	N	VAL- 177	2.75	148.46	H-Bond (Protein Donor)	false
O3B	OD2	ASP- 197	3.04	169.99	H-Bond (Ligand Donor)	false
O2B	OD2	ASP- 197	3.32	139	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 197	2.96	161.1	H-Bond (Ligand Donor)	false
O2B	NH2	ARG- 199	3.4	125.54	H-Bond (Protein Donor)	false
O2B	NE	ARG- 199	2.59	174.33	H-Bond (Protein Donor)	false
C5B	CB	ALA- 256	4.49	0	Hydrophobic	false
C1B	CB	ALA- 256	4.48	0	Hydrophobic	false