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Receptor
PDB id Resolution Class Description Source Keywords
4D06 2 Å EC: 5.5.1.6 BACTERIAL CHALCONE ISOMERASE COMPLEXED WITH NARINGENIN EUBACTERIUM RAMULUS ISOMERASE BACTERIAL CHALCONE ISOMERASE FLAVONOIDS NARINGE
Ref.: STRUCTURE AND CATALYTIC MECHANISM OF THE EVOLUTIONA UNIQUE BACTERIAL CHALCONE ISOMERASE ACTA CRYSTALLOGR.,SECT.D V. 71 907 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL E:402;
D:401;
D:403;
A:402;
F:401;
A:401;
E:404;
C:401;
E:403;
C:403;
B:402;
C:402;
D:402;
E:401;
F:403;
B:401;
F:402;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
35.453 Cl [Cl-]
X8W D:303;
B:301;
Valid;
Valid;
Atoms found LESS than expected: % Diff = 0;
none;
submit data
272.253 C15 H12 O5 c1cc(...
NAR D:301;
D:302;
F:302;
F:301;
A:301;
C:301;
E:301;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
Atoms found LESS than expected: % Diff = 0;
none;
none;
none;
none;
submit data
272.253 C15 H12 O5 c1cc(...
GOL F:303;
B:302;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4D06 2 Å EC: 5.5.1.6 BACTERIAL CHALCONE ISOMERASE COMPLEXED WITH NARINGENIN EUBACTERIUM RAMULUS ISOMERASE BACTERIAL CHALCONE ISOMERASE FLAVONOIDS NARINGE
Ref.: STRUCTURE AND CATALYTIC MECHANISM OF THE EVOLUTIONA UNIQUE BACTERIAL CHALCONE ISOMERASE ACTA CRYSTALLOGR.,SECT.D V. 71 907 2015
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4D06 - X8W C15 H12 O5 c1cc(ccc1/....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4D06 - X8W C15 H12 O5 c1cc(ccc1/....
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 4D06 - X8W C15 H12 O5 c1cc(ccc1/....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: X8W; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 X8W 1 1
2 HCC 0.568627 1
3 IPJ 0.490196 0.695652
4 HC4 0.488889 0.666667
Ligand no: 2; Ligand: NAR; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 CWE 1 1
2 NAR 1 1
3 SAK 0.65 0.870968
4 6JP 0.609375 0.848485
5 DFV 0.516667 0.928571
6 DFL 0.460317 0.857143
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4D06; Ligand: NAR; Similar sites found with APoc: 34
This union binding pocket(no: 1) in the query (biounit: 4d06.bio1) has 7 residues
No: Leader PDB Ligand Sequence Similarity
1 2Z1U ATP 1.06007
2 2BNE U5P 1.65975
3 2BNF UTP 1.65975
4 4KWD JF2 2.12014
5 5Z21 NAI 2.4735
6 5KOX RFP 2.82686
7 2IRY DGT 2.82686
8 4EDF UPG 2.82686
9 5EW9 5VC 2.95203
10 4LGY ADP 3.18021
11 1KPH 10A 3.18021
12 5VFC 9BA 3.18021
13 5EYK 5U5 3.26087
14 5EK3 5PK 3.53357
15 5JJU AMP 3.53357
16 4XYM COA 3.88693
17 4XZ3 COA 3.88693
18 1U3U NAD 4.24028
19 1U3U BNF 4.24028
20 1N46 PFA 4.26357
21 3JRX S1A 4.59364
22 9LDB NAD 4.59364
23 4L9I 8PR 4.59364
24 5IXG OTP 4.73373
25 2NU8 COA 4.947
26 1W96 S1A 5.65371
27 4Z87 GDP 7.06714
28 5CAE COA 7.66773
29 5CAE SIN 7.66773
30 5LXT GTP 8.12721
31 2CM4 RCL 8.66667
32 4F7E 0SH 14.2857
33 4FWE FAD 17.3145
34 4GUT FAD 17.3145
Pocket No.: 2; Query (leader) PDB : 4D06; Ligand: NAR; Similar sites found with APoc: 35
This union binding pocket(no: 2) in the query (biounit: 4d06.bio1) has 9 residues
No: Leader PDB Ligand Sequence Similarity
1 6FSG FMN None
2 2Y6Q FAD 1.76678
3 2YG3 FAD 2.12014
4 3G5N PB2 2.4735
5 3ICT FAD 2.4735
6 2GV8 FAD 2.4735
7 3ICS FAD 2.4735
8 1VQW FAD 2.4735
9 2RGJ FAD 2.4735
10 1H82 FAD 2.82686
11 1H82 GZZ 2.82686
12 2Z3Y F2N 3.18021
13 6F97 FAD 3.18021
14 6GAR FAD 3.53357
15 5JE0 AZ8 3.64372
16 5JE0 SAH 3.64372
17 2JB2 FAD 3.88693
18 2JB2 PHE 3.88693
19 3NKS FAD 4.24028
20 3AB1 FAD 4.24028
21 2UYQ SAM 4.59364
22 4HI0 GDP 5.52764
23 1RYI FAD 5.65371
24 1RYI GOA 5.65371
25 2QRY TPS 6.36042
26 1RP7 TZD 7.42049
27 5TS5 FAD 7.77385
28 3NUG NAD 8.48057
29 6F7L FAD 9.89399
30 6GAS FAD 11.3074
31 3LZW FAD 11.6608
32 3LZW NAP 11.6608
33 5BXQ GDP 13.3858
34 2NVA PL2 15.1943
35 2FTB OLA 26.4
Pocket No.: 3; Query (leader) PDB : 4D06; Ligand: X8W; Similar sites found with APoc: 11
This union binding pocket(no: 3) in the query (biounit: 4d06.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
1 1KQN NAD 2.50896
2 1FP6 ADP 3.18021
3 2XGT NSS 3.18021
4 5CPS GLC GLC GLC GLC GLC GLC GLC GLC GLC 3.18021
5 5CPS GLC GLC GLC GLC GLC GLC GLC GLC 3.18021
6 1M5B BN1 5.32319
7 1B7H LYS NLE LYS 6.00707
8 1MLY ACZ PLP 10.2473
9 4NG2 OHN 15.0442
10 4NTM 2K8 23.9669
11 1R4A GNP 33.3333
Pocket No.: 4; Query (leader) PDB : 4D06; Ligand: NAR; Similar sites found with APoc: 133
This union binding pocket(no: 4) in the query (biounit: 4d06.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 2BOS GLA GAL None
2 2BOS GLA GAL GLC None
3 2WKQ FMN 1.76678
4 2XMY CDK 2.12014
5 2XK9 XK9 2.12014
6 3PQB VGP 2.12014
7 4D4U FUC NDG GAL FUC 2.12014
8 4YVN EBS 2.12014
9 5YBN AKG 2.12014
10 4OJ8 AKG 2.12014
11 1QIN GIP 2.18579
12 5WKR NAR 2.24215
13 2P7Q GG6 2.25564
14 5A65 TPP 2.30415
15 6B3P GLC GLC GLC GLC 2.39234
16 6GW4 CHO 2.4735
17 5YB7 ORN 2.4735
18 4U03 GTP 2.4735
19 4J36 FAD 2.4735
20 2ET1 GLV 2.48756
21 3MTX PGT 2.64901
22 3PG7 PTY 2.73438
23 1MEX RAC 2.7907
24 1SZ0 M6P 2.82686
25 5UWA 8ND 2.95567
26 6HDT BTN 3.00752
27 1Y0G 8PP 3.14136
28 5GLT BGC GAL NAG GAL 3.18021
29 2Q0D ATP 3.18021
30 2MPR BGC GLC GLC 3.18021
31 1ZHX HC3 3.18021
32 2GC0 PAN 3.19149
33 1LN1 DLP 3.27103
34 5OF1 SAL 3.33333
35 5KEW 6SB 3.47222
36 5X7Q ACR 3.53357
37 4G31 0WH 3.53357
38 5INJ 6C7 3.53357
39 5TPU TYD 3.59712
40 3EW2 BTN 3.7037
41 4Z28 BTN 3.73134
42 3ZXE PGZ 3.7594
43 5HA0 LTD 3.84615
44 5DRB 5FJ 3.88693
45 1GP6 QUE 3.88693
46 1GP6 DH2 3.88693
47 1GP6 SIN 3.88693
48 5LUN OGA 3.88693
49 5XVG 8FX 3.88693
50 5XEG AKG 3.8961
51 5JSP DQY 3.9801
52 3L5R 47X 4.09836
53 4HK8 XYP XYP XYP XYP XYP XYP 4.2328
54 3Q8G PEE 4.24028
55 2AOT 2PM 4.24028
56 4M1U A2G MBG 4.28571
57 4JH6 FCN 4.34783
58 5BU3 4W9 4.34783
59 5DG2 GAL GLC 4.44444
60 2JIG PD2 4.46429
61 3SCH TB6 4.54545
62 2CET PGI 4.59364
63 5AE9 OKO 4.59364
64 1ULE GLA GAL NAG 4.66667
65 3AMN CBK 4.90566
66 3AMN CBI 4.90566
67 4YZC STU 4.947
68 3RWP ABQ 4.947
69 1OFL NGK GCD 4.947
70 2VFT SOR 4.947
71 5HCY 60D 4.947
72 1H8S AIC 4.947
73 4CNO 9PY 5.15873
74 2JDR GLY ARG PRO ARG THR THR SER PHE ALA GLU 5.30035
75 2JDR L20 5.30035
76 3E2M E2M 5.40541
77 2GJ5 VD3 5.55556
78 1ZB6 DIN 5.65371
79 2WA4 069 5.65371
80 3E8N ATP 5.65371
81 3E8N VRA 5.65371
82 1ZB6 GST 5.65371
83 3W8X FTK 5.65371
84 4MNS 2AX 5.66038
85 1J3R 6PG 5.78947
86 2A1L PCW 5.92593
87 1NKI PPF 5.92593
88 3W68 VIV 6.01504
89 4JNJ BTN 6.08696
90 5DKK FMN 6.2069
91 4WVW SLT 6.25
92 3VV1 GAL FUC 6.25
93 2IUW AKG 6.30252
94 4QXB OGA 6.36042
95 4AZP A9M 6.52174
96 1ZZ7 S0H 6.56566
97 4IMO PWZ 6.81818
98 4IAW LIZ 6.91489
99 1SQI 869 7.06714
100 1VA6 P2S 7.06714
101 3T2W BTN 7.37705
102 4Q9M FPP 7.72358
103 3FW4 CAQ 7.86517
104 4K55 H6P 8.06452
105 5ACM MBT 8.10811
106 6MPT C30 8.12721
107 4NPL AKG 8.4
108 1T27 PCW 8.48709
109 2Z77 HE7 8.63309
110 2QL9 CIT 8.67052
111 2E56 MYR 9.02778
112 4B2Z P5S 9.54064
113 5AIG VPR 9.6
114 6GVZ CHO 9.89399
115 3HUJ AGH 10.101
116 3E7O 35F 10.6007
117 5VX9 FUC GAL NAG GAL BGC 11.1801
118 5DJT FMN 11.4754
119 6BHQ NAG NAG FUL BMA MAN MAN NAG GAL 11.6071
120 1UU6 BGC BGC BGC BGC 11.6071
121 1UNB AKG 12.0141
122 1UNB PN1 12.0141
123 3PUR 2HG 12.3675
124 3T0W DIW 13.0081
125 4RYV ZEA 13.5484
126 6GNO XDI 14.0741
127 5NLD LBT 14.3885
128 3HCH RSM 16.4384
129 1N5S ADL 17.8571
130 1MHC FME TYR PHE ILE ASN ILE LEU THR LEU 18.1818
131 3WUD GLC GAL 19.1176
132 3STK PLM 21.2121
133 2HO2 PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU 23.6842
Pocket No.: 5; Query (leader) PDB : 4D06; Ligand: X8W; Similar sites found with APoc: 13
This union binding pocket(no: 5) in the query (biounit: 4d06.bio1) has 8 residues
No: Leader PDB Ligand Sequence Similarity
1 3BXO UPP 1.67364
2 6B9T 2HE 2.12014
3 1OZ0 MS1 3.53357
4 4MVK ACE VAL PHE PHE ALA GLU ASP NH2 4.25532
5 2HJ3 FAD 4.8
6 1EZ0 NAP 4.947
7 3MBG FAD 5.7554
8 3O55 FAD 6.4
9 1OQC FAD 6.4
10 2Q8M FBP 6.71378
11 1XC6 GAL 8.12721
12 2QL9 GLN GLY HIS GLY GLU 8.67052
13 5JHD GLY ILE LEU GLY PHE VAL PHE THR LEU 10
Pocket No.: 6; Query (leader) PDB : 4D06; Ligand: NAR; Similar sites found with APoc: 43
This union binding pocket(no: 6) in the query (biounit: 4d06.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 4LIT AKG 2.12014
2 6B9T 2HE 2.12014
3 2GWH PCI 2.4735
4 6B9R 2HE 2.4735
5 5H9Y BGC BGC BGC BGC 2.4735
6 3ZGJ RMN 2.4735
7 4J36 1HR 2.4735
8 2D6M LBT 2.51572
9 5NBW 8SK 2.7027
10 5EO8 TFU 3.18021
11 4QDF 30Q 3.18021
12 5H9Q TD2 3.22581
13 5TPV TYD 3.26797
14 5VX5 FUC GAL NAG GAL BGC 3.7037
15 2HFN FMN 3.92157
16 4GGZ BTN 4.34783
17 3GM5 CIT 4.40252
18 5AE2 FYC 4.59364
19 3ZW2 GAL FUC 4.5977
20 4YUS FMN 4.947
21 5MBC FMN 4.947
22 2GPT TLA 4.97132
23 1W6O LAT 5.22388
24 1SWG BTN 5.46875
25 5YEE LAB 5.88235
26 5L9B AKG 5.95238
27 5T9C G3P 5.97015
28 2DDQ HRB 6.57277
29 1X8D RNS 6.73077
30 3FW3 ETS 6.76692
31 2NNQ T4B 6.87023
32 2ZSC BTN 7.0922
33 3KFF XBT 8.64198
34 3KFF ZBT 8.64198
35 5TFZ 7BC 8.66667
36 4FHT DHB 8.9172
37 5I0U DCY 9
38 4MA6 28E 12.7389
39 5B09 4MX 14.4231
40 2BYC FMN 14.5985
41 1T0S BML 16.2791
42 6FA4 D1W 21.3873
43 1X0P FAD 27.2727
Pocket No.: 7; Query (leader) PDB : 4D06; Ligand: NAR; Similar sites found with APoc: 39
This union binding pocket(no: 7) in the query (biounit: 4d06.bio1) has 8 residues
No: Leader PDB Ligand Sequence Similarity
1 5F1H 5U6 None
2 6GNF ADP 1.41343
3 3LL5 ADP 1.60643
4 3LL5 IPE 1.60643
5 3VPH OXM 1.76678
6 2Y6Q I7T 1.76678
7 1MV8 NAD 2.12014
8 3OJO NAD 2.12014
9 4KVL PLM 2.4735
10 2CDC NAP 2.82686
11 2CDC XYP 2.82686
12 1WP4 NDP 2.82686
13 1C1X NAD 2.82686
14 1YKF NAP 3.18021
15 5XVH NAP 3.18021
16 1P0F NAP 3.18021
17 1DSS NAD 3.18021
18 5UR0 NAD 3.53357
19 1J0X NAD 3.88693
20 5OCM NAP 3.88693
21 1KOL NAD 3.88693
22 3ABI NAD 4.24028
23 1DLJ NAI 4.24028
24 1DLJ UGA 4.24028
25 3V1Y NAD 4.59364
26 9LDT NAD 4.59364
27 2OJW ADP 5.30035
28 4UXL 5P8 5.30035
29 5GVL GI8 7.06714
30 5GVL PLG 7.06714
31 2IMI GSH 7.23982
32 2B5W NAP 7.42049
33 1V97 MTE 7.42049
34 4MIG G3F 7.77385
35 4A34 FUL 8.16327
36 1GV0 NAD 8.48057
37 1RM4 NDP 9.54064
38 4X3R 686 10.2473
39 3H0L ADP 13.8298
Pocket No.: 8; Query (leader) PDB : 4D06; Ligand: NAR; Similar sites found with APoc: 20
This union binding pocket(no: 8) in the query (biounit: 4d06.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 1A78 TDG None
2 3SAO NKN 1.875
3 3SAO DBH 1.875
4 5O9W AKG 2.4735
5 1URX AAL GAL AAL GLA 3.19149
6 5HZX 2GE 3.40909
7 1JU4 BEZ 3.53357
8 5XIO HFG 3.88693
9 4RF7 ARG 4.24028
10 3OYW TDG 5.22388
11 1GZW GAL BGC 5.22388
12 4CPH LH4 5.51181
13 6D61 4AA 5.64103
14 3I4X DST 6.00707
15 2HZQ STR 6.32184
16 3A76 SPD 6.71378
17 1VA6 ADP 7.06714
18 1OGX EQU 7.63359
19 4N7C AEF 9.65909
20 6BU0 IHP 16.0305
Pocket No.: 9; Query (leader) PDB : 4D06; Ligand: NAR; Similar sites found with APoc: 8
This union binding pocket(no: 9) in the query (biounit: 4d06.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 3MPB FRU 3.65854
2 3LVW GSH 5.30035
3 3GFZ FMN 5.30035
4 3HAV ATP 5.65371
5 5L9V OGA 5.95238
6 2OVW CBI 6.00707
7 1IS3 LAT 7.40741
8 2AXR ABL 10.6007
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