scPDB - 1nd5 entry

Protein Data Bank Entry:

PDB ID : 1nd5

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2002-12-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Prostatic acid phosphatase
ID:	PPAP_HUMAN
AC:	P15309
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.1.3.2

Chains:

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

Ligand binding site composition:

B-Factor:	20.058
Number of residues:	25
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.125	334.125

% Hydrophobic	% Polar
57.58	42.42
According to VolSite

Ligand :

HET Code:	2BF
Formula:	C14H15NO3P
Molecular weight:	276.248 g/mol
DrugBank ID:	DB03577
Buried Surface Area:	67.81 %
Polar Surface area:	89.61 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	1
Rings:	2
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
67.0269	116.199	10.6394

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
O2P	CZ	ARG- 3010	3.33	0	Ionic (Protein Cationic)	false
O3P	CZ	ARG- 3010	3.5	0	Ionic (Protein Cationic)	false
O2P	NH2	ARG- 3010	2.63	121.16	H-Bond (Protein Donor)	false
O2P	NH2	ARG- 3014	3.17	140.93	H-Bond (Protein Donor)	false
O2P	NE	ARG- 3014	2.96	155.83	H-Bond (Protein Donor)	false
O2P	CZ	ARG- 3014	3.5	0	Ionic (Protein Cationic)	false
C4	CD1	ILE- 3017	3.7	0	Hydrophobic	false
C10	CD1	ILE- 3017	3.47	0	Hydrophobic	false
O1P	NH2	ARG- 3078	2.75	141.5	H-Bond (Protein Donor)	false
O1P	NE	ARG- 3078	3.01	136.28	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 3078	3.27	0	Ionic (Protein Cationic)	false
C2	CE2	TYR- 3122	3.3	0	Hydrophobic	false
C12	CB	SER- 3174	3.89	0	Hydrophobic	false
C11	CB	SER- 3174	3.52	0	Hydrophobic	false
C12	CB	ASP- 3178	3.74	0	Hydrophobic	false
O1P	ND1	HIS- 3256	2.71	155.58	H-Bond (Protein Donor)	false
C6	CB	HIS- 3256	3.62	0	Hydrophobic	false
O3P	N	ASP- 3257	2.72	169.06	H-Bond (Protein Donor)	false
N	OD1	ASP- 3257	3.52	0	Ionic (Ligand Cationic)	false
N	OD2	ASP- 3257	3.71	0	Ionic (Ligand Cationic)	false
C6	CG2	THR- 3258	4.08	0	Hydrophobic	false