scPDB - 1pjc entry

Protein Data Bank Entry:

PDB ID : 1pjc

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 1998-06-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Alanine dehydrogenase
ID:	O52942_PHOLP
AC:	O52942
Organism:	Phormidium lapideum
Reign:	Bacteria
TaxID:	32060
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	37.699
Number of residues:	43
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.010	678.375

% Hydrophobic	% Polar
42.79	57.21
According to VolSite

Ligand :

HET Code:	NAD
Formula:	C21H26N7O14P2
Molecular weight:	662.417 g/mol
DrugBank ID:	-
Buried Surface Area:	62.04 %
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
15.6375	12.3938	19.9153

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
O2N	OG	SER- 133	3.24	165.69	H-Bond (Protein Donor)	false
C5N	CB	SER- 133	4.31	0	Hydrophobic	false
C4N	CB	ALA- 136	3.63	0	Hydrophobic	false
O2A	N	VAL- 177	2.86	160.69	H-Bond (Protein Donor)	false
O1N	N	VAL- 178	2.99	164.92	H-Bond (Protein Donor)	false
C5D	CG2	VAL- 178	3.79	0	Hydrophobic	false
O3B	OD1	ASP- 197	2.69	161.76	H-Bond (Ligand Donor)	false
O2B	OD1	ASP- 197	3.35	130.88	H-Bond (Ligand Donor)	false
O2B	OD2	ASP- 197	2.69	155.64	H-Bond (Ligand Donor)	false
N1A	OG	SER- 219	2.83	161.77	H-Bond (Protein Donor)	false
O3D	O	VAL- 238	2.85	170.47	H-Bond (Ligand Donor)	false
C5B	CB	LEU- 239	3.89	0	Hydrophobic	false
C3D	CB	LEU- 239	3.63	0	Hydrophobic	false
C2D	CD1	LEU- 239	3.72	0	Hydrophobic	false
C5D	CB	LEU- 239	4.14	0	Hydrophobic	false
C3N	CG1	VAL- 266	3.82	0	Hydrophobic	false
N7N	O	VAL- 266	3.46	156.9	H-Bond (Ligand Donor)	false
C4D	CB	ALA- 267	4.35	0	Hydrophobic	false
O7N	N	MET- 300	2.82	149.69	H-Bond (Protein Donor)	false
O1N	O	HOH- 503	2.67	179.97	H-Bond (Protein Donor)	false