scPDB - 3dt4 entry

Protein Data Bank Entry:

PDB ID : 3dt4

Resolution :1.450 Å

Experimental Method : X-ray

Deposition Date : 2008-07-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
ID:	PCKGC_RAT
AC:	P07379
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	4.1.1.32

Chains:

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

Ligand binding site composition:

B-Factor:	6.754
Number of residues:	44
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	2
Water Molecules:	3
Cofactors:
Metals:	MN MN

Cavity properties

Ligandability	Volume (Å3)
0.103	536.625

% Hydrophobic	% Polar
43.40	56.60
According to VolSite

Ligand :

HET Code:	GTP
Formula:	C10H12N5O14P3
Molecular weight:	519.149 g/mol
DrugBank ID:	DB04137
Buried Surface Area:	71.58 %
Polar Surface area:	335.56 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
5.45969	-1.50287	45.6381

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
O3G	N	ALA- 287	2.99	145.3	H-Bond (Protein Donor)	false
O3B	N	ALA- 287	2.83	137.86	H-Bond (Protein Donor)	false
C5'	CB	ALA- 287	4.1	0	Hydrophobic	false
O1B	N	CYS- 288	3.42	143.36	H-Bond (Protein Donor)	false
O1B	N	GLY- 289	3.12	126.88	H-Bond (Protein Donor)	false
O3A	N	GLY- 289	3.01	151.73	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 290	2.78	157.82	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 290	2.78	152.39	H-Bond (Protein Donor)	false
O1B	N	LYS- 290	2.8	154.45	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 290	2.78	0	Ionic (Protein Cationic)	false
O1B	NZ	LYS- 290	2.78	0	Ionic (Protein Cationic)	false
O2B	N	THR- 291	2.81	156.11	H-Bond (Protein Donor)	false
O2A	ND2	ASN- 292	2.9	173.46	H-Bond (Protein Donor)	false
O2A	N	ASN- 292	3	157.8	H-Bond (Protein Donor)	false
C5'	CB	VAL- 335	4.37	0	Hydrophobic	false
C3'	CG1	VAL- 335	4.25	0	Hydrophobic	false
O3'	O	PRO- 337	2.78	174.25	H-Bond (Ligand Donor)	false
O1G	NH1	ARG- 405	3	154.9	H-Bond (Protein Donor)	false
O3G	NH2	ARG- 405	2.86	164.88	H-Bond (Protein Donor)	false
O3G	NH1	ARG- 405	3.39	134.91	H-Bond (Protein Donor)	false
O3G	CZ	ARG- 405	3.58	0	Ionic (Protein Cationic)	false
O6	N	PHE- 530	2.98	174.77	H-Bond (Protein Donor)	false
C2'	CE1	PHE- 530	4.17	0	Hydrophobic	false
O6	ND2	ASN- 533	3.18	147.95	H-Bond (Protein Donor)	false
O2G	MN	MN- 700	2.24	0	Metal Acceptor	false
O1G	MN	MN- 800	2.15	0	Metal Acceptor	false
O2B	MN	MN- 800	2.2	0	Metal Acceptor	false
N3	O	HOH- 1187	2.96	179.98	H-Bond (Protein Donor)	false