Receptor
PDB id Resolution Class Description Source Keywords
1XPM 1.6 Å EC: 2.3.3.10 CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS HMG-COA SYNTHASE WITH HMG-COA AND ACETOACETYL-COA AND ACETYLATED CYSTEINE STAPHYLOCOCCUS AUREUS SUBSP. AUREUS HMG-COA SYNTHASE HMGS COENZYME A THIOLASE FOLD CONDENSING ENZYME CHOLESTEROL BIOSYNTHESIS TRANSFERASE
Ref.: 3-HYDROXY-3-METHYLGLUTARYL-COA SYNTHASE INTERMEDIATE COMPLEX OBSERVED IN "REAL-TIME" PROC.NATL.ACAD.SCI.USA V. 47 16442 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CAA A:1402;
B:2402;
C:3402;
D:4402;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
851.607 C25 H40 N7 O18 P3 S CC(=O...
HMG A:1401;
B:2401;
C:3401;
D:4401;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
906.62 C27 H39 N7 O20 P3 S C[C@]...
SO4 A:1501;
A:1502;
B:2501;
B:2502;
C:3501;
C:3502;
D:4501;
D:4502;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1XPM 1.6 Å EC: 2.3.3.10 CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS HMG-COA SYNTHASE WITH HMG-COA AND ACETOACETYL-COA AND ACETYLATED CYSTEINE STAPHYLOCOCCUS AUREUS SUBSP. AUREUS HMG-COA SYNTHASE HMGS COENZYME A THIOLASE FOLD CONDENSING ENZYME CHOLESTEROL BIOSYNTHESIS TRANSFERASE
Ref.: 3-HYDROXY-3-METHYLGLUTARYL-COA SYNTHASE INTERMEDIATE COMPLEX OBSERVED IN "REAL-TIME" PROC.NATL.ACAD.SCI.USA V. 47 16442 2004
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1XPM - HMG C27 H39 N7 O20 P3 S C[C@](CC(=....
2 1XPL - CAA C25 H40 N7 O18 P3 S CC(=O)CC(=....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1XPM - HMG C27 H39 N7 O20 P3 S C[C@](CC(=....
2 1XPL - CAA C25 H40 N7 O18 P3 S CC(=O)CC(=....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1XPM - HMG C27 H39 N7 O20 P3 S C[C@](CC(=....
2 1XPL - CAA C25 H40 N7 O18 P3 S CC(=O)CC(=....
3 5HWP - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
4 5HWQ - CAA C25 H40 N7 O18 P3 S CC(=O)CC(=....
5 5HWO - HMG C27 H39 N7 O20 P3 S C[C@](CC(=....
6 5HWR - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
7 2WYA - HMG C27 H39 N7 O20 P3 S C[C@](CC(=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: CAA; Similar ligands found: 140
No: Ligand ECFP6 Tc MDL keys Tc
1 CAA 1 1
2 MLC 0.912 0.988506
3 1VU 0.880952 0.977273
4 ACO 0.879032 0.977273
5 1HE 0.867188 0.966292
6 3HC 0.867188 1
7 BCO 0.867188 0.988506
8 IVC 0.867188 1
9 SCA 0.853846 0.988506
10 3KK 0.850394 0.988506
11 COS 0.848 0.965909
12 CAO 0.848 0.955056
13 HGG 0.847328 0.988506
14 2MC 0.844961 0.945055
15 SOP 0.84375 0.965909
16 OXK 0.84375 0.988506
17 FAQ 0.840909 0.988506
18 CO6 0.837209 0.988506
19 HXC 0.834586 0.966292
20 GRA 0.834586 0.988506
21 TGC 0.828358 0.977273
22 MC4 0.825758 0.934783
23 CO8 0.822222 0.966292
24 FYN 0.821705 0.988372
25 COO 0.818182 0.988506
26 MCA 0.818182 0.977273
27 5F9 0.816176 0.966292
28 DCC 0.816176 0.966292
29 MFK 0.816176 0.966292
30 MYA 0.816176 0.966292
31 UCC 0.816176 0.966292
32 ST9 0.816176 0.966292
33 COK 0.815385 0.965909
34 0T1 0.809524 0.965517
35 COA 0.809524 0.988372
36 CMC 0.80916 0.965909
37 DCA 0.808 0.943182
38 COW 0.80597 0.977273
39 1GZ 0.80597 0.977273
40 BYC 0.80597 0.988506
41 IRC 0.80597 1
42 30N 0.804688 0.904255
43 CS8 0.804348 0.955556
44 BCA 0.8 0.977273
45 HDC 0.798561 0.966292
46 A1S 0.796992 0.965909
47 ETB 0.793651 0.910112
48 COF 0.792593 0.944444
49 AMX 0.790698 0.976744
50 YNC 0.787234 0.977273
51 2CP 0.785185 0.955056
52 SCO 0.784615 0.965517
53 CMX 0.784615 0.965517
54 2NE 0.782609 0.966292
55 1CZ 0.782609 0.977273
56 3CP 0.779412 0.965909
57 2KQ 0.779412 0.966292
58 FCX 0.778626 0.933333
59 FAM 0.778626 0.94382
60 4CA 0.773723 0.955056
61 HAX 0.772727 0.94382
62 WCA 0.765957 0.966292
63 SCD 0.762963 0.965517
64 CAJ 0.762963 0.94382
65 MCD 0.761194 0.94382
66 CA6 0.761194 0.876289
67 4KX 0.760563 0.955556
68 CCQ 0.757143 0.945055
69 CIC 0.757143 0.965909
70 NMX 0.755556 0.893617
71 MRS 0.755245 0.966292
72 MRR 0.755245 0.966292
73 1CV 0.753521 0.988506
74 4CO 0.751773 0.955056
75 0FQ 0.751773 0.965909
76 DAK 0.75 0.955556
77 0ET 0.746479 0.944444
78 01A 0.746479 0.923913
79 8Z2 0.744828 0.955556
80 CA8 0.741007 0.895833
81 YE1 0.73913 0.954545
82 UOQ 0.736111 0.944444
83 NHW 0.736111 0.944444
84 NHM 0.736111 0.944444
85 HFQ 0.731034 0.944444
86 1HA 0.724832 0.966292
87 NHQ 0.722973 0.977012
88 UCA 0.722581 0.966292
89 S0N 0.72028 0.94382
90 01K 0.72 0.965909
91 COT 0.715232 0.965909
92 CA3 0.694805 0.965909
93 CA5 0.683544 0.923913
94 CO7 0.678322 0.988506
95 93P 0.658385 0.955056
96 COD 0.656716 0.976744
97 93M 0.648485 0.955056
98 HMG 0.64 0.954545
99 PLM COA 0.631579 0.933333
100 COA PLM 0.631579 0.933333
101 COA MYR 0.631579 0.933333
102 5TW 0.62069 0.924731
103 4BN 0.62069 0.924731
104 OXT 0.618497 0.924731
105 JBT 0.594444 0.905263
106 BSJ 0.570621 0.934066
107 PAP 0.544715 0.802326
108 191 0.538462 0.876289
109 ACE SER ASP ALY THR NH2 COA 0.510638 0.922222
110 SFC 0.508982 0.966292
111 RFC 0.508982 0.966292
112 PPS 0.507812 0.744681
113 A3P 0.495935 0.790698
114 0WD 0.489933 0.78022
115 PTJ 0.439716 0.862069
116 3AM 0.435484 0.77907
117 3OD 0.429577 0.816092
118 PUA 0.427673 0.811111
119 A22 0.427536 0.804598
120 A2D 0.421875 0.793103
121 PAJ 0.421429 0.873563
122 SAP 0.41791 0.818182
123 ATR 0.41791 0.790698
124 AGS 0.41791 0.818182
125 OAD 0.415493 0.816092
126 ADP 0.412214 0.813953
127 A2R 0.410072 0.804598
128 NA7 0.405594 0.848837
129 BA3 0.40458 0.793103
130 ATP 0.402985 0.813953
131 AP5 0.401515 0.793103
132 B4P 0.401515 0.793103
133 ADQ 0.401408 0.795455
134 48N 0.401316 0.8
135 AQP 0.4 0.813953
136 2A5 0.4 0.837209
137 ME8 0.4 0.833333
138 AR6 0.4 0.793103
139 APR 0.4 0.793103
140 5FA 0.4 0.813953
Ligand no: 2; Ligand: HMG; Similar ligands found: 116
No: Ligand ECFP6 Tc MDL keys Tc
1 HMG 1 1
2 PLM COA 0.788732 0.955056
3 COA PLM 0.788732 0.955056
4 COA MYR 0.788732 0.955056
5 CCQ 0.68 0.923913
6 1VU 0.653061 0.933333
7 3HC 0.644295 0.954545
8 CAA 0.64 0.954545
9 3KK 0.639456 0.94382
10 IVC 0.633333 0.954545
11 1HE 0.633333 0.923077
12 MLC 0.633333 0.965909
13 BCO 0.633333 0.94382
14 ACE SER ASP ALY THR NH2 COA 0.629214 0.965909
15 ACO 0.62585 0.933333
16 SCA 0.625 0.965909
17 OXK 0.624161 0.965909
18 HGG 0.620915 0.965909
19 FAQ 0.616883 0.94382
20 2MC 0.615894 0.903226
21 1CZ 0.615385 0.955056
22 MC4 0.614379 0.913979
23 HXC 0.612903 0.923077
24 GRA 0.612903 0.965909
25 COS 0.612245 0.922222
26 CAO 0.612245 0.912088
27 CO6 0.609272 0.94382
28 TGC 0.608974 0.955056
29 COO 0.607843 0.94382
30 FYN 0.606667 0.943182
31 CO8 0.605096 0.923077
32 COK 0.602649 0.922222
33 30N 0.601351 0.864583
34 5F9 0.601266 0.923077
35 MFK 0.601266 0.923077
36 MYA 0.601266 0.923077
37 DCC 0.601266 0.923077
38 UCC 0.601266 0.923077
39 ST9 0.601266 0.923077
40 1GZ 0.6 0.933333
41 MCA 0.597403 0.955056
42 CS8 0.59375 0.913043
43 SOP 0.592105 0.922222
44 HDC 0.590062 0.923077
45 BYC 0.589744 0.94382
46 COW 0.589744 0.933333
47 2KQ 0.589744 0.944444
48 IRC 0.589744 0.954545
49 CMC 0.588235 0.94382
50 BCA 0.585987 0.933333
51 2CP 0.583333 0.933333
52 YNC 0.582822 0.933333
53 FAM 0.582781 0.901099
54 COA 0.581081 0.943182
55 0T1 0.581081 0.921348
56 A1S 0.580645 0.922222
57 COF 0.579618 0.902174
58 DCA 0.578231 0.9
59 4CA 0.575949 0.912088
60 2NE 0.575 0.923077
61 CIC 0.575 0.94382
62 1CV 0.574074 0.965909
63 3CP 0.56962 0.94382
64 AMX 0.569536 0.931818
65 NMX 0.567742 0.873684
66 ETB 0.567568 0.868132
67 MRR 0.567073 0.923077
68 MRS 0.567073 0.923077
69 CMX 0.565789 0.943182
70 SCO 0.565789 0.943182
71 WCA 0.564417 0.923077
72 SCD 0.564103 0.943182
73 DAK 0.563636 0.913043
74 FCX 0.562092 0.912088
75 4KX 0.560976 0.913043
76 8Z2 0.560241 0.913043
77 HAX 0.558442 0.901099
78 CAJ 0.55414 0.922222
79 01K 0.552941 0.922222
80 0FQ 0.552147 0.922222
81 4CO 0.552147 0.912088
82 NHM 0.551515 0.902174
83 UOQ 0.551515 0.902174
84 NHW 0.551515 0.902174
85 CA6 0.551282 0.838384
86 MCD 0.551282 0.922222
87 0ET 0.548781 0.902174
88 01A 0.548781 0.882979
89 NHQ 0.544379 0.932584
90 HFQ 0.538922 0.902174
91 1HA 0.538012 0.923077
92 YE1 0.5375 0.911111
93 UCA 0.533708 0.923077
94 CA8 0.530864 0.857143
95 COD 0.530201 0.954023
96 CO7 0.52795 0.94382
97 COT 0.522988 0.922222
98 S0N 0.518072 0.922222
99 CA3 0.508475 0.922222
100 CA5 0.502762 0.882979
101 93M 0.502703 0.933333
102 93P 0.5 0.933333
103 4BN 0.476923 0.884211
104 5TW 0.476923 0.884211
105 OXT 0.474227 0.904255
106 JBT 0.465 0.885417
107 ATP A A A 0.452055 0.781609
108 BSJ 0.441624 0.913043
109 A A A 0.427586 0.825581
110 UOC COA 0.423313 0.733333
111 PAP 0.42029 0.761364
112 ADP BMA 0.408163 0.816092
113 A3P 0.407407 0.75
114 AHZ 0.406452 0.813187
115 191 0.405714 0.857143
116 ADP PO3 0.4 0.790698
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1XPM; Ligand: CAA; Similar sites found: 22
This union binding pocket(no: 1) in the query (biounit: 1xpm.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4U5I BXP 0.01856 0.41671 2.27273
2 1Z03 OCH 0.03274 0.40492 2.77778
3 1XI9 PLP 0.0204 0.41158 3.0303
4 3HYW DCQ 0.03021 0.40878 3.28283
5 4CCW VKC 0.01649 0.41349 3.34448
6 3TDC 0EU 0.01806 0.40392 3.53535
7 5IXG OTP 0.01183 0.40083 3.5503
8 5AWV GHP 3MY 3FG GHP GHP OMY 3FG NAG MAN 0.02008 0.40907 3.78788
9 3FIU POP 0.02709 0.40932 4.41767
10 1TJY PAV 0.01525 0.42251 5.06329
11 2P9H IPT 0.02653 0.40185 5.57621
12 2INV FRU FRU 0.04198 0.40068 6.06061
13 3H78 BE2 0.000006786 0.49514 6.56566
14 1HZP DAO 0.002031 0.42884 7.76119
15 3OBK PBG 0.01497 0.4068 7.82828
16 5KAX RHQ 0.034 0.40405 9.63855
17 1OW4 2AN 0.01826 0.41002 13.1783
18 2VWA PTY 0.005757 0.44283 20.7921
19 1EBL COA 0.001068 0.4035 23.9748
20 5BNS 4VM 0.00008201 0.46314 24.6057
21 3IL6 B83 0.001169 0.40501 29.9065
22 5BQS 4VN 0.0004326 0.47023 30.031
Pocket No.: 2; Query (leader) PDB : 1XPM; Ligand: CAA; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 1xpm.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1XPM; Ligand: HMG; Similar sites found: 23
This union binding pocket(no: 3) in the query (biounit: 1xpm.bio1) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3CQL NAG 0.03931 0.40199 2.46914
2 1Z03 OCH 0.03625 0.40382 2.77778
3 4BG4 ARG 0.02906 0.40867 2.80899
4 2WT9 NIO 0.008385 0.4388 2.97872
5 4CCW VKC 0.01736 0.41349 3.34448
6 3TDC 0EU 0.01887 0.40392 3.53535
7 5AWV GHP 3MY 3FG GHP GHP OMY 3FG NAG MAN 0.02108 0.40907 3.78788
8 3FIU POP 0.02915 0.40887 4.41767
9 2G2Y MLI 0.01922 0.40795 5.19481
10 2VDF OCT 0.007081 0.4361 5.55556
11 3GQT UFO 0.0207 0.40487 6.31313
12 3H78 BE2 0.000001111 0.52944 6.56566
13 1HZP DAO 0.0004177 0.45384 7.76119
14 3OBK PBG 0.01698 0.4055 7.82828
15 5KAX RHQ 0.02083 0.41667 9.63855
16 2QS8 MET 0.005095 0.44396 10.3535
17 1TV5 A26 0.02589 0.40368 10.3535
18 3KYQ DPV 0.03548 0.40432 12.0603
19 1OW4 2AN 0.00897 0.4269 13.1783
20 2GUE NAG 0.01382 0.41602 14.7541
21 2VWA PTY 0.00688 0.44036 20.7921
22 5BNS 4VM 0.0001557 0.44739 24.6057
23 5BQS 4VN 0.0003589 0.47559 30.031
Pocket No.: 4; Query (leader) PDB : 1XPM; Ligand: HMG; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 1xpm.bio1) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 1XPM; Ligand: CAA; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 1xpm.bio2) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 1XPM; Ligand: HMG; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 1xpm.bio2) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 1XPM; Ligand: HMG; Similar sites found: 6
This union binding pocket(no: 7) in the query (biounit: 1xpm.bio2) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3MPB FRU 0.01776 0.40456 2.43902
2 2WMC MGP 0.01945 0.41616 3.93258
3 3BMN AX3 0.04808 0.40248 4.16667
4 5FRE SIA GAL 0.01543 0.42143 5.15464
5 4JD3 COA 0.00816 0.40242 8.08081
6 1MFA GLA MMA ABE 0.04627 0.40018 11.811
Pocket No.: 8; Query (leader) PDB : 1XPM; Ligand: CAA; Similar sites found: 5
This union binding pocket(no: 8) in the query (biounit: 1xpm.bio2) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1JL0 PUT 0.01169 0.40974 2.39521
2 3MPB FRU 0.01754 0.4007 2.43902
3 3BMN AX3 0.04167 0.40248 4.16667
4 5TVM PUT 0.02541 0.40653 7.05882
5 1MFA GLA MMA ABE 0.0395 0.40018 11.811
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