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Receptor
PDB id Resolution Class Description Source Keywords
3NY4 1.22 Å EC: 3.5.2.6 CRYSTAL STRUCTURE OF BLAC-K73A BOUND WITH CEFAMANDOLE MYCOBACTERIUM TUBERCULOSIS PENICILLIN BINDING PROTEIN BETA-LACTAM COMPLEX HYDROLASE-ACOMPLEX
Ref.: STRUCTURES OF THE MICHAELIS COMPLEX (1.2 A) AND THE ACYL INTERMEDIATE (2.0 A) OF CEFAMANDOLE BOUND IN T SITES OF THE MYCOBACTERIUM TUBERCULOSIS BETA-LACTAM AND E166A MUTANTS. BIOCHEMISTRY V. 49 9685 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PO4 A:1;
Invalid;
none;
submit data
94.971 O4 P [O-]P...
SMX A:308;
A:309;
A:310;
A:311;
A:312;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
submit data
462.503 C18 H18 N6 O5 S2 Cn1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3NY4 1.22 Å EC: 3.5.2.6 CRYSTAL STRUCTURE OF BLAC-K73A BOUND WITH CEFAMANDOLE MYCOBACTERIUM TUBERCULOSIS PENICILLIN BINDING PROTEIN BETA-LACTAM COMPLEX HYDROLASE-ACOMPLEX
Ref.: STRUCTURES OF THE MICHAELIS COMPLEX (1.2 A) AND THE ACYL INTERMEDIATE (2.0 A) OF CEFAMANDOLE BOUND IN T SITES OF THE MYCOBACTERIUM TUBERCULOSIS BETA-LACTAM AND E166A MUTANTS. BIOCHEMISTRY V. 49 9685 2010
Members (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 38 families.
1 6B68 - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
2 6B6F - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
3 6B69 - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
4 6B6A - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
5 4QB8 - 1TE C16 H21 N3 O4 S2 C[C@@H]1[C....
6 6B6C - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
7 6B6D - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
8 3NY4 - SMX C18 H18 N6 O5 S2 Cn1c(nnn1)....
9 6B6E - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
70% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 32 families.
1 6B68 - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
2 6B6F - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
3 6B69 - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
4 6B6A - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
5 4QB8 - 1TE C16 H21 N3 O4 S2 C[C@@H]1[C....
6 6B6C - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
7 6B6D - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
8 3NY4 - SMX C18 H18 N6 O5 S2 Cn1c(nnn1)....
9 6B6E - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
50% Homology Family (42)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 5EOE - CIT C6 H8 O7 C(C(=O)O)C....
2 5EOO - CIT C6 H8 O7 C(C(=O)O)C....
3 3BFF - FPM C12 H15 N O5 S C[C@H]([C@....
4 5UJ3 - CE4 C14 H15 N5 O6 S2 CO/N=C(/c1....
5 5UJ4 - SFR C12 H17 N O6 S C[C@H]([C@....
6 6B68 - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
7 6B6F - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
8 6B69 - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
9 6B6A - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
10 4QB8 - 1TE C16 H21 N3 O4 S2 C[C@@H]1[C....
11 6B6C - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
12 6B6D - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
13 3NY4 - SMX C18 H18 N6 O5 S2 Cn1c(nnn1)....
14 6B6E - 9F2 C18 H18 N8 O7 S3 CN1C(=NC(=....
15 6CYU - CE4 C14 H15 N5 O6 S2 CO/N=C(/c1....
16 5TWE - CAZ C17 H19 N5 O7 S2 CC(C)(C(=O....
17 4XXR - JSC C22 H17 N2 O6 Ru S CC1([C@@H]....
18 3G31 Ki = 1.3 mM GF1 C12 H15 N O4 C[C@@H](C(....
19 3G34 Ki = 1.1 mM 1CE C12 H12 N6 O S C1CCc2c(c3....
20 3HLW - CE3 C16 H17 N5 O7 S2 CC(=O)OCC1....
21 3G30 Ki = 3.1 mM G30 C11 H9 F2 N O3 c1cc(c(cc1....
22 6CYQ - CE4 C14 H15 N5 O6 S2 CO/N=C(/c1....
23 3HVF - PNK C16 H20 N2 O5 S CC1([C@@H]....
24 3G32 Ki = 0.194 mM 3G3 C11 H9 N5 O2 c1ccc2c(c1....
25 3G2Z Ki = 4.4 mM GZ2 C7 H9 N5 O C1CC(=CC(=....
26 6BU3 Ki = 0.28 uM 3GK C16 H10 F3 N7 O c1cc(cc(c1....
27 3G35 Ki = 0.021 mM F13 C14 H10 F N5 O c1cc(cc(c1....
28 5FQJ - 6NT C6 H4 N4 O2 c1cc2c(cc1....
29 5FQK Kd = 15.8 uM 6NT C6 H4 N4 O2 c1cc2c(cc1....
30 5NE2 Ki = 84 pM DGL C5 H9 N O4 C(CC(=O)O)....
31 2ZD8 - MER C17 H27 N3 O5 S C[C@@H]1[C....
32 1VM1 - TAZ C10 H12 N4 O5 S C[C@@]1([C....
33 3MKE - CZ6 C16 H25 B N4 O6 S B1(O[C@H](....
34 4FH2 - 0RN C8 H11 N O5 S CC1([C@@H]....
35 3SOI - CIT C6 H8 O7 C(C(=O)O)C....
36 2Y91 - 98J C5 H8 O4 C(CO)C(=O)....
37 1PZP Ki = 480 uM FTA C16 H13 N7 c1ccc(cc1)....
38 1PZO Ki = 460 uM CBT C15 H13 Cl2 N5 c1cc(ccc1C....
39 1NY0 - NBF C14 H16 B N O4 B(CNC(=O)c....
40 1NXY - SM2 C14 H14 B N O5 S B([C@H](c1....
41 3P98 - CIT C6 H8 O7 C(C(=O)O)C....
42 1W7F - ICT C6 H8 O7 C([C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SMX; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 SMX 1 1
2 4KO 0.404959 0.848837
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3NY4; Ligand: SMX; Similar sites found with APoc: 76
This union binding pocket(no: 1) in the query (biounit: 3ny4.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 4WEY EG6 1.0582
2 3LDW ZOL 1.13208
3 4RC8 STE 1.8018
4 3L9W AMP 1.88679
5 6EKZ SNP 1.88679
6 3ZS7 ATP 1.88679
7 3K87 FAD 2.16216
8 5IXK 6EW 2.19298
9 3BZ3 YAM 2.26415
10 1N20 3AG 2.26415
11 2WOE AR6 2.26415
12 3FPF MTA 2.64151
13 3FPF TNA 2.64151
14 5EK3 5PK 2.64151
15 3OTX AP5 2.64151
16 2GMH UQ5 2.64151
17 3A51 VDY 2.64151
18 5K53 STE 2.67176
19 5UWA 8ND 2.95567
20 3MMH SME 2.99401
21 3GZ9 D32 3.01887
22 4Q6R 30J 3.01887
23 3E5A VX6 3.01887
24 2YOO K2B 3.01887
25 4MN7 SME 3.3557
26 3FC4 EDO 3.39623
27 1GNI OLA 3.39623
28 2DSA GSH 3.44828
29 2DSA HPX 3.44828
30 2W3L DRO 3.47222
31 6AYH C3G 3.48259
32 1U1F 183 3.51562
33 2Y88 2ER 3.68852
34 1RDT L79 3.71901
35 1LBT T80 3.77358
36 1BUC CAA 3.77358
37 5NM7 GLY 3.77358
38 3E3U NVC 4.06091
39 1RM0 NAI 4.15094
40 3QMK SGN IDS SGN IDS 4.20561
41 1RYI FAD 4.5283
42 2QJY SMA 4.90566
43 1OPK MYR 4.90566
44 5DQW ADP 5.21327
45 6GBX S77 5.28302
46 1PN4 HDC 5.28302
47 2PX8 MGT 5.57621
48 3SJH LAR 6.03774
49 3VRV YSD 6.03774
50 4QWT ACD 6.03774
51 4XF6 ADP 6.41509
52 4XF6 INS 6.41509
53 4XF6 LIP 6.41509
54 1A27 EST 6.41509
55 3WCA FPS 6.41509
56 1FK5 OLA 6.45161
57 2VHW NAI 6.79245
58 6H3O FAD 7.16981
59 5V3Y 5V8 7.16981
60 4DSG FAD 7.54717
61 4DSG UDP 7.54717
62 3D9F FAD 7.92453
63 3D9F N6C 7.92453
64 2X5W K2B 7.92453
65 5OSW DIU 9.0566
66 2IFB PLM 9.92366
67 5LWY OLB 10.2804
68 5X8G S0N 10.9434
69 4QO5 NAG 11.6981
70 5Y6Q MCN 11.6981
71 1ML6 GBX 12.6697
72 5K52 OCD 13.2075
73 3RMK BML 13.253
74 3CXH SMA 14.1732
75 4CA5 3EF 15.0943
76 3V66 D3A 15.4717
Pocket No.: 2; Query (leader) PDB : 3NY4; Ligand: SMX; Similar sites found with APoc: 1
This union binding pocket(no: 2) in the query (biounit: 3ny4.bio1) has 5 residues
No: Leader PDB Ligand Sequence Similarity
1 3QDL FMN None
Pocket No.: 3; Query (leader) PDB : 3NY4; Ligand: SMX; Similar sites found with APoc: 51
This union binding pocket(no: 3) in the query (biounit: 3ny4.bio1) has 51 residues
No: Leader PDB Ligand Sequence Similarity
1 6BKK 308 None
2 1XX6 ADP None
3 1R1Q ACE ARG GLU PTR VAL ASN VAL None
4 6BKL EU7 None
5 2RC8 DSN 1.50943
6 5A04 BGC 1.88679
7 6B2W AG2 1.88679
8 2WCI GSH 2.22222
9 1WUU GLA 2.26415
10 5ME4 HP4 3.01887
11 3WMX THR 3.01887
12 3ESS 18N 3.04348
13 4GYS MLI 3.22061
14 5TQZ GLC 3.33333
15 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 3.39623
16 1YQS BSA 3.39623
17 2OVW CBI 3.39623
18 4K91 SIN 3.77358
19 3HUN ZZ7 3.77358
20 3PDB PMP 3.77358
21 3R75 BEZ 3.77358
22 3PD6 PMP 3.77358
23 6A4R ASP 3.77358
24 3IHB GLU 4.15094
25 4KQR VPP 4.15094
26 2EFX NFA 4.15094
27 2FB3 MET 4.15094
28 4YG6 GAL NAG 4.29448
29 4YKI GLY 4.29688
30 2FN1 SAL 4.5283
31 2RCA GLY 4.90566
32 4RKX 3S9 4.90566
33 5NC1 NAG 5.06329
34 1QSC ACE TYR PRO ILE GLN GLU THR 5.2356
35 1VBO MAN MAN MAN 5.36913
36 1VBO MAN 5.36913
37 3MAN BMA BMA MAN 5.66038
38 4DNJ ANN 5.66038
39 2EB5 OXL 5.66038
40 1WDN GLN 5.75221
41 6HQD SRT 6.41509
42 4CP8 MLI 7.80287
43 3N7S 3N7 7.82609
44 1PIG GLC GLC 7.92453
45 3WCS MAN NAG GAL 8.26772
46 1M32 PLP 9.0566
47 2AK5 ARG PRO PRO LYS PRO ARG PRO ARG 9.375
48 5XH2 NPO 11.4504
49 4LO6 SIA GAL 12.1053
50 4XFR CIT 13.2075
51 5KXE 6Y2 16.4609
Pocket No.: 4; Query (leader) PDB : 3NY4; Ligand: SMX; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 3ny4.bio1) has 1 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 3NY4; Ligand: SMX; Similar sites found with APoc: 7
This union binding pocket(no: 5) in the query (biounit: 3ny4.bio1) has 49 residues
No: Leader PDB Ligand Sequence Similarity
1 2YJP CYS 2.26415
2 3TUR DGL 3.01887
3 4GK9 MAN BMA MAN MAN MAN 3.01887
4 6HT0 GQ8 3.22581
5 4OKE AMP 3.57143
6 2AJH MET 4.08163
7 4JZ8 CIT 13.9623
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