scPDB - 4p5a entry

Protein Data Bank Entry:

PDB ID : 4p5a

Resolution :1.760 Å

Experimental Method : X-ray

Deposition Date : 2014-03-15

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Flavin-dependent thymidylate synthase
ID:	C1IC19_STRCI
AC:	C1IC19
Organism:	Streptomyces cacaoi subsp. asoensis
Reign:	Bacteria
TaxID:	249586
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	30 %
B	33 %
D	37 %

Ligand binding site composition:

B-Factor:	13.343
Number of residues:	51
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	2
Water Molecules:	5
Cofactors:	FAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.296	2372.625

% Hydrophobic	% Polar
32.29	67.71
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	65.14 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
16.0896	26.2738	37.6156

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
N1	NH2	ARG- 86	3.19	121.32	H-Bond (Protein Donor)	false
O2	NH2	ARG- 86	2.79	174.08	H-Bond (Protein Donor)	false
C4'	CB	ARG- 86	4.04	0	Hydrophobic	false
O2A	N	ARG- 88	2.92	168.42	H-Bond (Protein Donor)	false
O2A	NE	ARG- 88	2.76	176.08	H-Bond (Protein Donor)	false
O1P	NH2	ARG- 88	2.99	141.63	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 88	3.59	0	Ionic (Protein Cationic)	false
O1P	CZ	ARG- 88	3.95	0	Ionic (Protein Cationic)	false
O1A	OG1	THR- 89	3.13	157.59	H-Bond (Protein Donor)	false
C5B	CG2	THR- 89	4.13	0	Hydrophobic	false
C1B	CG2	THR- 89	4	0	Hydrophobic	false
O2	N	GLU- 94	2.72	163.97	H-Bond (Protein Donor)	false
N3	O	GLU- 94	2.88	154.74	H-Bond (Ligand Donor)	false
N1A	ND2	ASN- 182	2.99	176.02	H-Bond (Protein Donor)	false
C2B	CD	ARG- 184	4.24	0	Hydrophobic	false
O1P	NH2	ARG- 184	3.17	152.33	H-Bond (Protein Donor)	false
O2P	NH1	ARG- 184	2.92	129.03	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 184	3.97	0	Ionic (Protein Cationic)	false
O2P	CZ	ARG- 184	3.64	0	Ionic (Protein Cationic)	false
C8M	CB	LEU- 192	4.27	0	Hydrophobic	false
C5'	CD1	LEU- 192	4.26	0	Hydrophobic	false
C8M	CD	ARG- 193	4.21	0	Hydrophobic	false
C1B	C4B	FAD- 302	4.12	0	Hydrophobic	false
C4B	C1B	FAD- 302	4.05	0	Hydrophobic	false
O2'	O	HOH- 420	2.83	179.95	H-Bond (Protein Donor)	false
O2'	O	HOH- 477	2.72	152.53	H-Bond (Ligand Donor)	false