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Receptor
PDB id Resolution Class Description Source Keywords
5KZD 2.33 Å EC: 4.1.3.3 N-ACETYLNEURAMINATE LYASE FROM METHICILLIN-RESISTANT STAPHYL AUREUS WITH BOUND SIALIC ACID ALDITOL STAPHYLOCOCCUS AUREUS (STRAIN USA300) TIM-BARREL INHIBITOR N-ACETYLNEURAMINATE LYASE LYASE
Ref.: STRUCTURE AND INHIBITION OF N-ACETYLNEURAMINATE LYA METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS. FEBS LETT. V. 590 4414 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
RCJ A:301;
B:301;
C:301;
D:301;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Ki = 0.39 mM
311.286 C11 H21 N O9 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5KZD 2.33 Å EC: 4.1.3.3 N-ACETYLNEURAMINATE LYASE FROM METHICILLIN-RESISTANT STAPHYL AUREUS WITH BOUND SIALIC ACID ALDITOL STAPHYLOCOCCUS AUREUS (STRAIN USA300) TIM-BARREL INHIBITOR N-ACETYLNEURAMINATE LYASE LYASE
Ref.: STRUCTURE AND INHIBITION OF N-ACETYLNEURAMINATE LYA METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS. FEBS LETT. V. 590 4414 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5KZD Ki = 0.39 mM RCJ C11 H21 N O9 CC(=O)N[C@....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4IMF - SI3 C11 H19 N O9 CC(=O)N[C@....
2 4IMG - NGF C11 H19 N O10 C([C@@H]([....
3 1F73 Ki = 4.1 mM HMN C11 H21 N O9 CC(=O)N[C@....
4 1F74 Ki = 0.9 mM NAY C11 H19 N O8 CC(=O)N[C@....
5 5KZD Ki = 0.39 mM RCJ C11 H21 N O9 CC(=O)N[C@....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2WPB Ki = 1.3 mM ZZI C10 H21 N O4 CCCN(CCC)C....
2 2WNZ - LAC C3 H6 O3 C[C@H](C(=....
3 2XFW - PYR C3 H4 O3 CC(=O)C(=O....
4 2WKJ - PYR C3 H4 O3 CC(=O)C(=O....
5 4IMF - SI3 C11 H19 N O9 CC(=O)N[C@....
6 4IMG - NGF C11 H19 N O10 C([C@@H]([....
7 1F73 Ki = 4.1 mM HMN C11 H21 N O9 CC(=O)N[C@....
8 1F74 Ki = 0.9 mM NAY C11 H19 N O8 CC(=O)N[C@....
9 5KZD Ki = 0.39 mM RCJ C11 H21 N O9 CC(=O)N[C@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: RCJ; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 RCJ 1 1
2 HMN 1 1
3 WQP 0.6 0.733333
4 SI3 0.568627 0.970588
5 RSH 0.454545 0.647059
6 NGF 0.421053 0.888889
7 MN9 0.403846 0.941176
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5KZD; Ligand: RCJ; Similar sites found with APoc: 112
This union binding pocket(no: 1) in the query (biounit: 5kzd.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 2PK4 ACA None
2 4H6Q TFB 0.682594
3 4H6Q FAD 0.682594
4 3OID NDP 1.55039
5 3NUG NAD 2.02429
6 4J4H NAI 2.3166
7 4J4H 1J1 2.3166
8 2Q2V NAD 2.35294
9 1Q8V MAN MAN MAN 2.38095
10 2PHX MAN MAN 2.38095
11 1Q8Q MAN MMA 2.38095
12 2GND MAN 2.38095
13 1FDJ 13P 2.38908
14 3C3D FO1 2.38908
15 3FXU TSU 2.38908
16 3JYN NDP 2.38908
17 2G37 FAD 2.38908
18 2E5V FAD 2.73038
19 2E2P ADP 3.07167
20 2DUR MAN MAN 3.16206
21 2RI1 GLP 3.40426
22 1GQ2 NAP 3.41297
23 4X7R NTO 3.41297
24 4RVU NDP 3.41297
25 3VZS NAP 3.50195
26 4K7O EKZ 3.57143
27 2QGI UDP 3.62903
28 1AE1 NAP 3.663
29 1JXZ BCA 3.71747
30 2Z48 NGA 3.75427
31 1GZ4 ATP 3.75427
32 1TLL NAP 3.75427
33 4H8N NDP 3.75427
34 2DM6 NAP 3.75427
35 2DM6 IMN 3.75427
36 3KIV ACA 3.79747
37 3ZLR X0B 3.79747
38 5K6A NAP 3.81944
39 4CMI NAP 3.81944
40 3BMN NAP 3.81944
41 5JCJ NAP 3.81944
42 4CLR NAP 3.81944
43 5JDI NAP 3.81944
44 4CM4 NAP 3.81944
45 4CM9 NAP 3.81944
46 5JDC NAP 3.81944
47 3BMO NAP 3.81944
48 3JQ9 NAP 3.81944
49 3JQF NAP 3.81944
50 3BMQ NAP 3.81944
51 3JQ8 NAP 3.81944
52 4CM8 NAP 3.81944
53 3JQG NAP 3.81944
54 3JQA NAP 3.81944
55 4CME NAP 3.81944
56 2BQP GLC 3.84615
57 5M42 FMN 3.94265
58 3GDN FAD 4.09556
59 3GDN HBX 4.09556
60 6D61 4AA 4.10256
61 2VZ0 D64 4.10448
62 2VZ0 NAP 4.10448
63 2WD7 NAP 4.10448
64 1VL8 NAP 4.11985
65 5IN3 G1P 4.43686
66 4NMC 2OP 4.43686
67 4NMC FAD 4.43686
68 1H3F TYE 4.77816
69 3Q9T FAY 4.77816
70 4GPS CIT 4.77816
71 3WG6 NDP 4.77816
72 4IF4 BEF 4.80769
73 6FOG OXL 4.91071
74 3CF6 SP1 5.11945
75 4A62 ANP 5.11945
76 5ABH YWN 5.11945
77 5KF6 FAD 5.11945
78 1JAC AMG 5.26316
79 1QF9 ADP 5.6701
80 1QF9 ALF 5.6701
81 1QF9 C5P 5.6701
82 4DC2 ADE 5.80205
83 1JOT GAL A2G 6.01504
84 1H5Q NAP 6.03774
85 3G6M CFF 6.48464
86 3QV1 NAD 6.82594
87 1VKF CIT 6.91489
88 4L80 OXL 7.16724
89 4DBH OXL 7.29167
90 1UKZ ADP 7.38916
91 1NC4 DOF 7.44186
92 1NC2 DOE 7.44186
93 5MB4 NAG 7.50853
94 1TIW FAD 7.84983
95 1TIW TFB 7.84983
96 4O8A FAD 7.84983
97 2BTO GTP 8.33333
98 5G41 AP5 8.52018
99 2FKA BEF 8.52713
100 1LSS NAD 8.57143
101 4AUT FAD 10.2389
102 4CS9 AMP 10.582
103 2OFD NGA 11.2676
104 1T9D P22 11.9454
105 6CI9 NAP 12.7413
106 6EV2 BGC 16.5899
107 4L9Z OXL 16.7235
108 5ITZ GTP 18.8976
109 5EYP GTP 26.6272
110 3I7S PYR 34.589
111 4PTN GXV 44.7099
112 1W3T 3GR 48.1229
Pocket No.: 2; Query (leader) PDB : 5KZD; Ligand: RCJ; Similar sites found with APoc: 57
This union binding pocket(no: 2) in the query (biounit: 5kzd.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 2PT9 2MH 1.36519
2 2PT9 S4M 1.36519
3 2I7C AAT 1.41343
4 1YQZ FAD 2.04778
5 3WQT ANP 2.06612
6 4ZB8 GDS 2.25225
7 4GKY MAN 2.29885
8 4XQC NAD 2.38908
9 4XQC 13D 2.38908
10 1X1T NAD 2.69231
11 5LNQ CAA 2.73038
12 5UAV TFB 2.73038
13 5UAV NDP 2.73038
14 6HOY TSN 2.73038
15 6AIX A3P 2.73038
16 1MVQ MMA 2.9661
17 5VW2 FDA 3.07167
18 5VW2 NAP 3.07167
19 1QFY FAD 3.07167
20 1QFY NAP 3.07167
21 1X7D ORN 3.07167
22 3QDY A2G GAL 3.4965
23 4X7G 3Y8 3.58566
24 1AOE GW3 3.64583
25 1AOE NDP 3.64583
26 2Z48 A2G 3.75427
27 2UUU FAD 3.75427
28 2UUU PL3 3.75427
29 4M52 FAD 3.75427
30 2A8X FAD 3.75427
31 3JQ7 NAP 3.81944
32 1B74 DGN 4.33071
33 3K6V CIT 4.43686
34 6BQ6 TER 4.43686
35 3QFS NAP 4.43686
36 4PU6 ASP 4.58015
37 6AM8 PLT 4.77816
38 6AMI TRP 4.77816
39 5WGR FAD 4.77816
40 4JD3 COA 5.11945
41 3CV2 OXL 5.11945
42 5OC1 FAD 5.46075
43 1QPB TPP 5.46075
44 3KJS DQ1 5.46075
45 6C0B MLI 5.80205
46 2CVQ NDP 6.14334
47 5MDH NAD 6.48464
48 2C6Q NDP 6.48464
49 1FEC FAD 7.50853
50 1OMO NAD 8.87372
51 1FLJ GSH 9.23077
52 3FGZ BEF 9.375
53 2CDC XYS 9.55631
54 2CDC NAP 9.55631
55 2CDC XYP 9.55631
56 6H3O FAD 10.2389
57 5GT9 NAP 10.6464
Pocket No.: 3; Query (leader) PDB : 5KZD; Ligand: RCJ; Similar sites found with APoc: 63
This union binding pocket(no: 3) in the query (biounit: 5kzd.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 6BR7 BEF None
2 2BOS GLA GAL GLC None
3 2BOS GLA GAL GLC NBU None
4 5MW4 5JU 1.70648
5 6A46 DCM 1.95312
6 4YNU FAD 2.04778
7 4YNU LGC 2.04778
8 2J5V RGP 2.04778
9 2R75 01G 2.04778
10 1UKG MMA 2.38095
11 2PHW MAN MAN 2.38095
12 3CTY FAD 2.38908
13 1GVE NAP 2.38908
14 5T2U NAP 2.41935
15 6F97 FAD 2.73038
16 2UZH IPE 3.0303
17 4PQG NAG 3.07167
18 3DJL FAD 3.07167
19 2AMT GPP 3.14465
20 4RF2 NAP 3.30882
21 5THQ NDP 3.30882
22 1C3X 8IG 3.38346
23 1P7T PYR 3.41297
24 1D8C GLV 3.41297
25 1GPE FAD 3.41297
26 1LOJ U 3.44828
27 1LOJ URI 3.44828
28 1NZY BCA 3.71747
29 4Z24 FAD 3.75427
30 4EZD SEY 3.75427
31 2CUN 3PG 4.09556
32 4AT0 FAD 4.09556
33 2BSA NAP 4.43686
34 2RAB NAD 4.43686
35 2E7Z MGD 4.43686
36 5EB4 FAD 4.43686
37 1UJP CIT 4.79705
38 3DJF BC3 4.87805
39 5LV1 78T 5
40 5O4J PJL 5.10949
41 5O4J SAH 5.10949
42 5O4J 9KH 5.10949
43 2OEM 1AE 5.11945
44 6B5K TYD 5.11945
45 3FPZ AHZ 5.11945
46 2D7I UDP 5.11945
47 3ETG NDP 5.11945
48 3ETG GLU 5.11945
49 5A5W GUO 5.5336
50 1QX4 FAD 6.20438
51 2A0W DIH 6.57439
52 2AE2 NAP 6.92308
53 2AE2 PTO 6.92308
54 1O5O U5P 7.69231
55 5ECP JAA 9.41704
56 5ECP MET 9.41704
57 1L5Y BEF 10.3226
58 3IP8 B85 10.8871
59 4BC5 5FX 11.2628
60 4YG6 GAL NAG 12.8834
61 3WSG CIT 15.4762
62 1LES GLC FRU 17.3077
63 4ZOH MCN 20.8333
Pocket No.: 4; Query (leader) PDB : 5KZD; Ligand: RCJ; Similar sites found with APoc: 54
This union binding pocket(no: 4) in the query (biounit: 5kzd.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 1M3U KPL 1.51515
2 4FN4 NAD 1.5748
3 1O68 KIV 1.81818
4 4MIG G3F 2.04778
5 5EO8 TFU 2.04778
6 4WZH FMN 2.04778
7 2BD0 NAP 2.04918
8 2GND MAN MMA 2.38095
9 1Q8S MAN MMA 2.38095
10 2PHF MAN MAN 2.38095
11 1Q8P MAN MMA 2.38095
12 2PHU MAN MAN 2.38095
13 4WB6 ATP 2.38908
14 2QCS ANP 2.38908
15 6GW4 CHO 2.73038
16 5C9J DAO 3.20285
17 2Q1A 2KT 3.41297
18 1VMK GUN 3.61011
19 4IP7 FLC 3.75427
20 2Z49 AMG 3.75427
21 4MZU TDR 4.09556
22 3C3N FMN 4.09556
23 5FA6 FAD 4.43686
24 5FA6 NAP 4.43686
25 1V1A KDG 4.43686
26 3IT7 TLA 4.94506
27 5IFK HPA 5.11945
28 3HAZ FAD 5.11945
29 5UIU 8CG 5.11945
30 1C3M MAN MAN 5.44218
31 1TD2 PXL 5.57491
32 3VP6 HLD 5.80205
33 5XH2 NPO 6.10687
34 1NXJ TLA 6.55738
35 5HCT 61P 6.82594
36 5OKU 0L1 7.16724
37 3RUG DB6 7.35294
38 3ZUY TCH 7.43034
39 4O48 ASP 7.50853
40 4CCK OGA 7.84983
41 4Y3O OGA 7.84983
42 4CCN OGA 7.84983
43 5IVX ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 8.24742
44 1B8O IMH 8.80282
45 2VAR KDF 8.94569
46 4KCT PYR 9.55631
47 2F6U CIT 9.82906
48 3LGS ADE 10.1124
49 3LGS SAH 10.1124
50 3U1T MLI 10.5802
51 3MJY FMN 11.2628
52 3MJY IJZ 11.2628
53 3D3W NAP 15.1639
54 5HSA FAS 19.1126
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