scPDB - 1kc1 entry

Protein Data Bank Entry:

PDB ID : 1kc1

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2001-11-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	dTDP-4-dehydrorhamnose reductase
ID:	RMLD_SALTY
AC:	P26392
Organism:	Salmonella typhimurium
Reign:	Bacteria
TaxID:	99287
EC Number:	1.1.1.133

Chains:

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

Ligand binding site composition:

B-Factor:	35.772
Number of residues:	45
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.044	617.625

% Hydrophobic	% Polar
40.44	59.56
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	53.81 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
10.1668	-15.2954	17.0849

Binding mode :

What is Poseview ?

2D View
3D View

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
O2A	N	GLN- 11	3	161.63	H-Bond (Protein Donor)	false
O2N	NE2	GLN- 11	2.79	154.68	H-Bond (Protein Donor)	false
O1N	N	VAL- 12	3.09	167.13	H-Bond (Protein Donor)	false
C5D	CG2	VAL- 12	4.33	0	Hydrophobic	false
N6A	OD1	ASP- 39	3.09	136.4	H-Bond (Ligand Donor)	false
N1A	N	PHE- 40	2.87	143.5	H-Bond (Protein Donor)	false
C1B	CB	ALA- 62	4.35	0	Hydrophobic	false
C5B	CB	ALA- 63	4.47	0	Hydrophobic	false
C3D	CB	ALA- 63	3.88	0	Hydrophobic	false
O4B	N	ALA- 63	2.74	164.85	H-Bond (Protein Donor)	false
O1A	OG1	THR- 65	2.96	162.76	H-Bond (Protein Donor)	false
C5B	CG2	THR- 65	4.18	0	Hydrophobic	false
C2D	CG2	THR- 65	4.1	0	Hydrophobic	false
C4D	CB	TYR- 102	3.63	0	Hydrophobic	false
C5N	CB	THR- 104	3.89	0	Hydrophobic	false
O2D	OH	TYR- 128	2.8	144.36	H-Bond (Protein Donor)	false
O2D	NZ	LYS- 132	3.1	150.33	H-Bond (Protein Donor)	false
C5N	CG2	THR- 151	4.26	0	Hydrophobic	false
C3N	CB	VAL- 154	3.77	0	Hydrophobic	false
C4N	CG2	VAL- 154	4.13	0	Hydrophobic	false
O1N	O	HOH- 938	2.69	159.69	H-Bond (Protein Donor)	false