scPDB - 4m99 entry

Protein Data Bank Entry:

PDB ID : 4m99

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2013-08-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	UDP-N-acetylgalactosaminyltransferase
ID:	Q5FAE1_NEIG1
AC:	Q5FAE1
Organism:	Neisseria gonorrhoeae
Reign:	Bacteria
TaxID:	242231
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	62 %
C	38 %

Ligand binding site composition:

B-Factor:	51.045
Number of residues:	43
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.641	556.875

% Hydrophobic	% Polar
50.30	49.70
According to VolSite

Ligand :

HET Code:	ACO
Formula:	C23H34N7O17P3S
Molecular weight:	805.539 g/mol
DrugBank ID:	-
Buried Surface Area:	47.13 %
Polar Surface area:	429.68 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	20

Mass center Coordinates

X	Y	Z
-12.2965	-0.195235	-7.29329

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
CH3	CB	ASP- 332	4.12	0	Hydrophobic	false
S1P	CB	SER- 344	4.42	0	Hydrophobic	false
S1P	CG	PRO- 345	4.44	0	Hydrophobic	false
CH3	CG	PRO- 345	3.85	0	Hydrophobic	false
C2P	CB	SER- 350	4.23	0	Hydrophobic	false
O	N	GLY- 351	2.91	158.85	H-Bond (Protein Donor)	false
O5P	N	THR- 363	2.88	155.6	H-Bond (Protein Donor)	false
O1A	NH2	ARG- 368	3.22	145.06	H-Bond (Protein Donor)	false
O1A	NH1	ARG- 368	3.34	140.12	H-Bond (Protein Donor)	false
O3A	NH1	ARG- 368	2.91	149.11	H-Bond (Protein Donor)	false
OAP	NH1	ARG- 368	2.66	133.85	H-Bond (Protein Donor)	false
O1A	CZ	ARG- 368	3.71	0	Ionic (Protein Cationic)	false
CAP	CD	ARG- 368	4.1	0	Hydrophobic	false
C6P	CB	ARG- 368	4	0	Hydrophobic	false
N4P	OE1	GLN- 369	2.91	120.44	H-Bond (Ligand Donor)	false
CDP	CG2	THR- 378	4.36	0	Hydrophobic	false
N6A	O	ALA- 381	2.75	172.83	H-Bond (Ligand Donor)	false
O9P	N	ALA- 381	3.16	142.72	H-Bond (Protein Donor)	false
C2B	CG2	VAL- 386	4.18	0	Hydrophobic	false
CEP	CG2	THR- 394	4.4	0	Hydrophobic	false
O9A	NZ	LYS- 401	3.4	149.85	H-Bond (Protein Donor)	false
O9A	NZ	LYS- 401	3.4	0	Ionic (Protein Cationic)	false
C1B	CD1	LEU- 403	4.24	0	Hydrophobic	false
CCP	CD1	LEU- 403	3.96	0	Hydrophobic	false
CEP	CD1	LEU- 403	3.93	0	Hydrophobic	false
N8P	O	HOH- 606	3.27	153.04	H-Bond (Ligand Donor)	false
N1A	O	HOH- 624	2.68	179.94	H-Bond (Protein Donor)	false