scPDB - 4h1q entry

Protein Data Bank Entry:

PDB ID : 4h1q

Resolution :1.590 Å

Experimental Method : X-ray

Deposition Date : 2012-09-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Matrix metalloproteinase-9
ID:	MMP9_HUMAN
AC:	P14780
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.4.24.35

Chains:

Chain Name:	Percentage of Residues within binding site
A	12 %
B	88 %

Ligand binding site composition:

B-Factor:	16.156
Number of residues:	51
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	2
Water Molecules:	2
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.076	2720.250

% Hydrophobic	% Polar
44.91	55.09
According to VolSite

Ligand :

HET Code:	0XX
Formula:	C54H66N8O14S2
Molecular weight:	1115.277 g/mol
DrugBank ID:	-
Buried Surface Area:	46.95 %
Polar Surface area:	325.03 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	8
Rings:	5
Aromatic rings:	5
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	30

Mass center Coordinates

X	Y	Z
29.3065	-5.63808	25.7333

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
C38	CD2	LEU- 114	4.39	0	Hydrophobic	false
C24	CD1	LEU- 187	4.43	0	Hydrophobic	false
C26	CD1	LEU- 187	3.55	0	Hydrophobic	false
O14	N	LEU- 188	2.76	169.14	H-Bond (Protein Donor)	false
C3	CD1	LEU- 188	4.1	0	Hydrophobic	false
O14	N	ALA- 189	3.42	152.45	H-Bond (Protein Donor)	false
O36	N	ALA- 191	3.32	168.81	H-Bond (Protein Donor)	false
C38	CB	PRO- 193	4.06	0	Hydrophobic	false
C12	CB	LEU- 222	4.13	0	Hydrophobic	false
C4	CG1	VAL- 223	4.19	0	Hydrophobic	false
C13	CG2	VAL- 223	4.05	0	Hydrophobic	false
C13	CB	HIS- 226	3.79	0	Hydrophobic	false
C12	CB	HIS- 226	3.94	0	Hydrophobic	false
C31	CB	HIS- 230	3.7	0	Hydrophobic	false
N49	O	GLY- 233	3.16	123.13	H-Bond (Ligand Donor)	false
C67	CB	ASP- 235	4.12	0	Hydrophobic	false
C70	CB	ASP- 235	3.98	0	Hydrophobic	false
C47	CB	ASP- 235	4.06	0	Hydrophobic	false
C39	CB	ASP- 235	4.39	0	Hydrophobic	false
C42	CB	ASP- 235	4.34	0	Hydrophobic	false
C73	CB	ASP- 235	4.03	0	Hydrophobic	false
C71	CB	HIS- 236	4.42	0	Hydrophobic	false
C11	CD1	LEU- 243	3.77	0	Hydrophobic	false
C24	CE2	TYR- 245	3.48	0	Hydrophobic	false
C23	CB	PRO- 246	3.62	0	Hydrophobic	false
C23	CG	PRO- 246	3.36	0	Hydrophobic	false
C24	CB	MET- 247	4.29	0	Hydrophobic	false
C5	CB	TYR- 248	4.28	0	Hydrophobic	false
C8	CB	TYR- 248	4.12	0	Hydrophobic	false
O78	NE2	HIS- 266	3.33	131.71	H-Bond (Protein Donor)	false
C51	CD2	LEU- 267	4.37	0	Hydrophobic	false
O25	ZN	ZN- 301	2.11	0	Metal Acceptor	false
O23	ZN	ZN- 301	2.15	0	Metal Acceptor	false
O77	O	HOH- 446	2.93	120.53	H-Bond (Ligand Donor)	false