Receptor
PDB id Resolution Class Description Source Keywords
4ZYB 1.5 Å EC: 3.4.24.75 HIGH RESOLUTION STRUCTURE OF M23 PEPTIDASE LYTM WITH SUBSTRA ANALOGUE STAPHYLOCOCCUS AUREUS SUBSP. AUREUS NCORGANISM_TAXID: 93061 LYTM LYSOSTAPHIN PEPTIDOGLYCAN AMIDASE PEPTIDASE HYDROLATETRAGLYCINE PHOSPHINATE TRANSITION STATE ANALOGUE COMPLE
Ref.: HIGH RESOLUTION STRUCTURE OF AN M23 PEPTIDASE WITH SUBSTRATE ANALOGUE. SCI REP V. 5 14833 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA B:402;
D:402;
A:402;
C:402;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
 submit data
40.078 Ca [Ca+2...
ZN C:401;
A:401;
B:401;
D:401;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
 submit data
65.409 Zn [Zn+2...
UNL A:407;
A:405;
A:406;
C:403;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
n/a NULL NULL
EDO B:405;
A:408;
 Invalid;
Invalid;
 none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
CL D:403;
A:404;
A:403;
B:403;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
35.453 Cl [Cl-]
EPE C:405;
A:410;
 Invalid;
Invalid;
 none;
none;
 submit data
238.305 C8 H18 N2 O4 S C1CN(...
PEG B:404;
 Invalid;
 none;
 submit data
106.12 C4 H10 O3 C(COC...
4SQ B:406;
D:404;
A:409;
C:404;
 Valid;
Valid;
Valid;
Valid;
 Atoms found MORE than expected: % Diff = 1.278;
Atoms found MORE than expected: % Diff = 1.278;
Atoms found MORE than expected: % Diff = 1.278;
none;
 submit data
281.203 C8 H16 N3 O6 P C(CP(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4ZYB 1.5 Å EC: 3.4.24.75 HIGH RESOLUTION STRUCTURE OF M23 PEPTIDASE LYTM WITH SUBSTRA ANALOGUE STAPHYLOCOCCUS AUREUS SUBSP. AUREUS NCORGANISM_TAXID: 93061 LYTM LYSOSTAPHIN PEPTIDOGLYCAN AMIDASE PEPTIDASE HYDROLATETRAGLYCINE PHOSPHINATE TRANSITION STATE ANALOGUE COMPLE
Ref.: HIGH RESOLUTION STRUCTURE OF AN M23 PEPTIDASE WITH SUBSTRATE ANALOGUE. SCI REP V. 5 14833 2015
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4ZYB - 4SQ C8 H16 N3 O6 P C(CP(=O)(C....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4ZYB - 4SQ C8 H16 N3 O6 P C(CP(=O)(C....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4ZYB - 4SQ C8 H16 N3 O6 P C(CP(=O)(C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 4SQ; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 4SQ 1 1
2 GGG 0.416667 0.727273
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4ZYB; Ligand: 4SQ; Similar sites found: 22
This union binding pocket(no: 1) in the query (biounit: 4zyb.bio2) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3U2U UDP 0.03941 0.40649 None
2 5BVE 4VG 0.01833 0.44508 1.49254
3 1FNN ADP 0.01498 0.41195 2.98507
4 3OTX AP5 0.04696 0.4034 4.47761
5 1YNH SUO 0.03247 0.40243 4.47761
6 2YAK OSV 0.01284 0.42913 5.22388
7 5IQD GNP 0.02401 0.42138 5.97015
8 5IQD RIO 0.02506 0.42138 5.97015
9 3AHO 3A2 0.03179 0.4056 5.97015
10 1F52 ADP 0.01028 0.41202 6.71642
11 4FFG 0U8 0.009519 0.40605 6.71642
12 2A1L PCW 0.02532 0.42667 7.46269
13 1ZB6 GST 0.01775 0.42164 7.46269
14 1WUB OTP 0.04978 0.40943 7.46269
15 3E7O 35F 0.04719 0.40114 7.46269
16 5LNQ CAA 0.04212 0.40033 7.46269
17 2Q4H AMP 0.007674 0.43823 8.20895
18 2GFD RDA 0.0249 0.40706 8.20895
19 2IZ1 ATR 0.03747 0.40769 9.70149
20 2C49 ADN 0.004478 0.43666 10.4478
21 3IT7 TLA 0.00007488 0.5096 20.8955
22 2O3Z AI7 0.04738 0.42763 24.6269
Pocket No.: 2; Query (leader) PDB : 4ZYB; Ligand: 4SQ; Similar sites found: 4
This union binding pocket(no: 2) in the query (biounit: 4zyb.bio4) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1SMR PIV HIS PRO PHE HIS LPL TYR TYR SER 0.03439 0.40521 3.73134
2 3BZF VAL MET ALA PRO ARG ALA LEU LEU LEU 0.03168 0.405 6.18557
3 3EEB IHP 0.01117 0.40354 8.20895
4 5DM1 5D7 0.03275 0.41014 22.3881
Pocket No.: 3; Query (leader) PDB : 4ZYB; Ligand: 4SQ; Similar sites found: 20
This union binding pocket(no: 3) in the query (biounit: 4zyb.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5DRB 5FJ 0.04612 0.40232 None
2 2XMY CDK 0.02274 0.42985 1.49254
3 1LN1 DLP 0.0316 0.40046 2.23881
4 3E8N VRA 0.03768 0.4061 2.98507
5 3E8N ATP 0.03768 0.4061 2.98507
6 2GU8 796 0.03536 0.41438 3.73134
7 5K8B PDG 0.0172 0.40168 3.73134
8 5ECP JAA 0.02553 0.41313 5.22388
9 5ECP MET 0.02553 0.41313 5.22388
10 4FWE FAD 0.03669 0.40752 5.22388
11 2EQA AMP 0.01417 0.4088 5.97015
12 4CVZ TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 0.0258 0.4081 7.14286
13 5N87 N66 0.008214 0.43208 7.46269
14 5HSA FAS 0.04679 0.40035 8.20895
15 3HAZ FAD 0.02532 0.42972 8.95522
16 4X6F 3XU 0.04022 0.40114 10.4478
17 1Y0G 8PP 0.02417 0.41524 11.9403
18 4HA6 FAD 0.04555 0.4026 11.9403
19 5EOO CIT 0.00712 0.41716 13.4328
20 5VCV 1N1 0.01473 0.40648 19.403
Pocket No.: 4; Query (leader) PDB : 4ZYB; Ligand: 4SQ; Similar sites found: 7
This union binding pocket(no: 4) in the query (biounit: 4zyb.bio3) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2WK9 PLG 0.03543 0.40508 3.73134
2 1IZE IVA VAL VAL STA ALA STA 0.02353 0.40418 4.47761
3 3FRK TQP 0.03149 0.40667 5.22388
4 1QFY NAP 0.04805 0.40208 7.46269
5 1QFY FAD 0.04805 0.40208 7.46269
6 4XJC TTP 0.02324 0.40136 13.4328
7 5U23 TQP 0.03266 0.40584 19.403
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