scPDB - 1c1d entry

Protein Data Bank Entry:

PDB ID : 1c1d

Resolution :1.250 Å

Experimental Method : X-ray

Deposition Date : 1999-07-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Phenylalanine dehydrogenase
ID:	DHPH_RHOSO
AC:	Q59771
Organism:	Rhodococcus sp
Reign:	Bacteria
TaxID:	1831
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	17.442
Number of residues:	49
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:	K

Cavity properties

Ligandability	Volume (Å3)
1.054	702.000

% Hydrophobic	% Polar
44.23	55.77
According to VolSite

Ligand :

HET Code:	NAI
Formula:	C21H27N7O14P2
Molecular weight:	663.425 g/mol
DrugBank ID:	DB00157
Buried Surface Area:	60.46 %
Polar Surface area:	342.9 Å2

Number of
H-Bond Acceptors:	19
H-Bond Donors:	6
Rings:	5
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
21.5498	49.3705	-19.8374

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
O2D	NH2	ARG- 42	3.23	126.06	H-Bond (Protein Donor)	false
O2D	OD1	ASP- 118	2.87	157.23	H-Bond (Ligand Donor)	false
C3D	CG2	VAL- 119	3.92	0	Hydrophobic	false
O7N	OG	SER- 149	2.69	158.67	H-Bond (Protein Donor)	false
C4N	CG2	THR- 153	3.53	0	Hydrophobic	false
O2A	N	ALA- 185	2.99	178.24	H-Bond (Protein Donor)	false
O2N	N	VAL- 186	2.86	170.29	H-Bond (Protein Donor)	false
O3B	OD2	ASP- 205	3.48	122.32	H-Bond (Ligand Donor)	false
O3B	OD1	ASP- 205	2.69	158.88	H-Bond (Ligand Donor)	false
O2B	OD2	ASP- 205	2.81	164.68	H-Bond (Ligand Donor)	false
C1B	CB	ALA- 239	4.36	0	Hydrophobic	false
O3D	O	ALA- 239	2.9	150.71	H-Bond (Ligand Donor)	false
C5B	CE	MET- 240	4.35	0	Hydrophobic	false
C4D	CB	ALA- 261	4.35	0	Hydrophobic	false
O3D	N	ASN- 262	3.22	162.56	H-Bond (Protein Donor)	false
O2D	ND2	ASN- 262	2.88	140.31	H-Bond (Protein Donor)	false
C4N	CB	PHE- 361	4.14	0	Hydrophobic	false
O2N	O	HOH- 1163	2.77	172.08	H-Bond (Protein Donor)	false