scPDB - 1d4o entry

Protein Data Bank Entry:

PDB ID : 1d4o

Resolution :1.210 Å

Experimental Method : X-ray

Deposition Date : 1999-10-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NAD(P) transhydrogenase, mitochondrial
ID:	NNTM_BOVIN
AC:	P11024
Organism:	Bos taurus
Reign:	Eukaryota
TaxID:	9913
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	24.402
Number of residues:	46
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.475	607.500

% Hydrophobic	% Polar
52.78	47.22
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	67.5 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
18.3104	27.865	11.4105

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
C5B	CB	TYR- 31	4.2	0	Hydrophobic	false
O2N	N	TYR- 31	2.95	151.52	H-Bond (Protein Donor)	false
N7N	O	VAL- 63	3.02	148.35	H-Bond (Ligand Donor)	false
C2D	CG2	VAL- 63	3.62	0	Hydrophobic	false
O2N	N	GLY- 65	2.95	175.68	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 66	3.44	0	Ionic (Protein Cationic)	false
O2A	NH1	ARG- 66	2.97	142.95	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 66	3.04	139.39	H-Bond (Protein Donor)	false
N7N	O	MET- 67	3.32	145.09	H-Bond (Ligand Donor)	false
C4B	CB	ASN- 107	4.34	0	Hydrophobic	false
O1N	N	ASN- 107	2.86	162.35	H-Bond (Protein Donor)	false
O1A	N	ASP- 108	2.57	159.75	H-Bond (Protein Donor)	false
C3D	CB	ASP- 108	3.7	0	Hydrophobic	false
O1N	N	THR- 109	3.4	159.78	H-Bond (Protein Donor)	false
O1N	OG1	THR- 109	2.82	160.43	H-Bond (Protein Donor)	false
C5D	CG2	THR- 109	4.2	0	Hydrophobic	false
C1B	CB	LYS- 140	4.12	0	Hydrophobic	false
O2X	NZ	LYS- 140	2.75	162.8	H-Bond (Protein Donor)	false
O2X	NZ	LYS- 140	2.75	0	Ionic (Protein Cationic)	false
O1X	NH2	ARG- 141	3.03	154.94	H-Bond (Protein Donor)	false
O3X	N	ARG- 141	2.88	161.26	H-Bond (Protein Donor)	false
O3X	NE	ARG- 141	2.83	161.13	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 141	3.77	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 141	3.7	0	Ionic (Protein Cationic)	false
O2X	OG	SER- 142	2.78	157.24	H-Bond (Protein Donor)	false
O2X	N	SER- 142	3.01	132.08	H-Bond (Protein Donor)	false
O3B	O	VAL- 145	3.18	155.49	H-Bond (Ligand Donor)	false
O2A	N	TYR- 147	2.86	162.38	H-Bond (Protein Donor)	false
C4D	CB	TYR- 147	3.72	0	Hydrophobic	false
N6A	OD1	ASP- 166	3.09	159.98	H-Bond (Ligand Donor)	false
N1A	N	ALA- 167	2.91	148.57	H-Bond (Protein Donor)	false
N7N	O	HOH- 332	3.41	132.21	H-Bond (Ligand Donor)	false