scPDB - 1b5d entry

Protein Data Bank Entry:

PDB ID : 1b5d

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 1999-01-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Deoxycytidylate 5-hydroxymethyltransferase
ID:	DCHM_BPT4
AC:	P08773
Organism:	Enterobacteria phage T4
Reign:	Viruses
TaxID:	10665
EC Number:	2.1.2.8

Chains:

Chain Name:	Percentage of Residues within binding site
A	10 %
B	90 %

Ligand binding site composition:

B-Factor:	15.075
Number of residues:	34
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.541	958.500

% Hydrophobic	% Polar
35.92	64.08
According to VolSite

Ligand :

HET Code:	DCM
Formula:	C9H12N3O7P
Molecular weight:	305.181 g/mol
DrugBank ID:	-
Buried Surface Area:	65.73 %
Polar Surface area:	170.38 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	2
Rings:	2
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
30.8581	1.2376	-1.8571

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
O3P	NZ	LYS- 28	2.71	154.03	H-Bond (Protein Donor)	false
O3P	NZ	LYS- 28	2.71	0	Ionic (Protein Cationic)	false
O5'	NH2	ARG- 123	3.47	163.74	H-Bond (Protein Donor)	false
O1P	NE	ARG- 123	3.03	177.47	H-Bond (Protein Donor)	false
O3P	NH2	ARG- 123	3.06	137.57	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 123	3.82	0	Ionic (Protein Cationic)	false
O3P	CZ	ARG- 123	3.77	0	Ionic (Protein Cationic)	false
O2P	NE	ARG- 124	2.97	172.44	H-Bond (Protein Donor)	false
O2P	CZ	ARG- 124	3.71	0	Ionic (Protein Cationic)	false
C2'	SG	CYS- 148	3.81	0	Hydrophobic	false
C5'	SG	CYS- 148	3.68	0	Hydrophobic	false
O1P	NH1	ARG- 168	2.94	147.29	H-Bond (Protein Donor)	false
O1P	NH2	ARG- 168	3.39	130.72	H-Bond (Protein Donor)	false
O2P	NH1	ARG- 168	3.49	123.8	H-Bond (Protein Donor)	false
O2P	NH2	ARG- 168	2.72	149.53	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 168	3.59	0	Ionic (Protein Cationic)	false
O2P	CZ	ARG- 168	3.51	0	Ionic (Protein Cationic)	false
O1P	OG	SER- 169	2.73	163.18	H-Bond (Protein Donor)	false
C2'	CB	SER- 169	4.19	0	Hydrophobic	false
O2	ND2	ASN- 170	2.92	134.3	H-Bond (Protein Donor)	false
O2	N	ASP- 171	3	158.13	H-Bond (Protein Donor)	false
C2'	CB	ASP- 171	4.44	0	Hydrophobic	false
N3	OD2	ASP- 179	2.84	167.5	H-Bond (Protein Donor)	false
N4	OD2	ASP- 179	3.41	133.5	H-Bond (Ligand Donor)	false
N4	OD1	ASP- 179	2.93	169.26	H-Bond (Ligand Donor)	false
O3'	NE2	HIS- 216	2.78	176.22	H-Bond (Protein Donor)	false
O3'	OH	TYR- 218	2.71	143.25	H-Bond (Protein Donor)	false
N4	O	HOH- 401	3.49	157.33	H-Bond (Ligand Donor)	false
O2P	O	HOH- 403	2.6	179.97	H-Bond (Protein Donor)	false