Receptor
PDB id Resolution Class Description Source Keywords
4B2D 2.3 Å EC: 2.7.1.40 HUMAN PKM2 WITH L-SERINE AND FBP BOUND. HOMO SAPIENS TRANSFERASE TUMOUR PKM2 GLYCOLYSIS
Ref.: SERINE IS A NATURAL LIGAND AND ALLOSTERIC ACTIVATOR PYRUVATE KINASE M2 NATURE V. 491 458 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FBP A:600;
B:600;
C:600;
D:600;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
340.116 C6 H14 O12 P2 C([C@...
MG A:700;
C:700;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
SER A:1532;
B:1532;
C:1532;
D:1532;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd = 200 uM
105.093 C3 H7 N O3 C([C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4B2D 2.3 Å EC: 2.7.1.40 HUMAN PKM2 WITH L-SERINE AND FBP BOUND. HOMO SAPIENS TRANSFERASE TUMOUR PKM2 GLYCOLYSIS
Ref.: SERINE IS A NATURAL LIGAND AND ALLOSTERIC ACTIVATOR PYRUVATE KINASE M2 NATURE V. 491 458 2012
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4B2D Kd = 200 uM SER C3 H7 N O3 C([C@@H](C....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4B2D Kd = 200 uM SER C3 H7 N O3 C([C@@H](C....
50% 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 4B2D Kd = 200 uM SER C3 H7 N O3 C([C@@H](C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: FBP; Similar ligands found: 9
No: Ligand ECFP6 Tc MDL keys Tc
1 FBP 1 1
2 AFP 1 1
3 F1X 0.744186 0.954545
4 TA6 0.666667 0.954545
5 F6P 0.666667 0.954545
6 FDP 0.462963 0.954545
7 OI7 0.448276 0.976744
8 F1P 0.418182 0.847826
9 AHG 0.404255 0.930233
Ligand no: 2; Ligand: SER; Similar ligands found: 32
No: Ligand ECFP6 Tc MDL keys Tc
1 SER 1 1
2 DSN 1 1
3 DCY 0.65 0.84
4 CYS 0.65 0.84
5 ABA 0.6 0.692308
6 DBB 0.6 0.692308
7 2RA 0.6 0.75
8 HSE 0.590909 0.821429
9 C2N 0.571429 0.730769
10 ASN 0.545455 0.625
11 ASP 0.545455 0.714286
12 DAS 0.545455 0.714286
13 DAB 0.521739 0.724138
14 AS2 0.5 0.703704
15 LEU 0.5 0.642857
16 HCS 0.5 0.777778
17 NVA 0.5 0.62069
18 CSO 0.5 0.636364
19 API 0.5 0.633333
20 CSS 0.48 0.689655
21 DGY 0.47619 0.607143
22 DGL 0.461538 0.655172
23 GLU 0.461538 0.655172
24 GGL 0.461538 0.655172
25 ORN 0.444444 0.689655
26 SLZ 0.433333 0.625
27 UN1 0.413793 0.633333
28 DLY 0.413793 0.666667
29 11C 0.413793 0.633333
30 CME 0.40625 0.666667
31 DHH 0.4 0.612903
32 LYS 0.4 0.645161
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4B2D; Ligand: SER; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4b2d.bio1) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4B2D; Ligand: FBP; Similar sites found: 97
This union binding pocket(no: 2) in the query (biounit: 4b2d.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1TLL FMN 0.001949 0.43972 1.09489
2 5JCM FAD 0.0319 0.4167 1.33038
3 5JCM NAD 0.03273 0.4167 1.33038
4 5JCM ISD 0.03273 0.4167 1.33038
5 1T10 F6P 0.01329 0.41386 1.45985
6 2O2C G6Q 0.006601 0.40434 1.45985
7 1H82 GZZ 0.04623 0.40715 1.48305
8 1H82 FAD 0.0403 0.40715 1.48305
9 3PC3 P1T 0.007874 0.40854 1.70778
10 3L6C MLI 0.004482 0.43979 1.76991
11 1TE2 PGA 0.01085 0.41366 2.21239
12 1BH2 GSP 0.01329 0.40709 2.22222
13 1OBV FMN 0.0005721 0.4263 2.36686
14 4JWH SAH 0.002559 0.43597 2.55591
15 5MW4 5JU 0.004809 0.44201 2.69461
16 1G6H ADP 0.009763 0.42419 2.72374
17 4AMV F6R 0.005398 0.40822 2.73723
18 3OZG SSI 0.004612 0.41126 2.8
19 1J0D 5PA 0.002922 0.43645 2.93255
20 4H2D FMN 0.002314 0.41056 3.0303
21 5TTJ FAD 0.02232 0.40844 3.06122
22 1MJH ATP 0.002751 0.42932 3.08642
23 1I1N SAH 0.004789 0.42789 3.09735
24 4PPF FLC 0.001845 0.47125 3.14286
25 2X2T GAL NGA 0.01385 0.42269 3.26797
26 2DTJ THR 0.003594 0.42917 3.37079
27 3FJO FMN 0.001991 0.43377 3.46715
28 1KOJ PAN 0.006413 0.41081 3.46715
29 5FA6 FMN 0.02277 0.42826 3.64964
30 5FA6 FAD 0.02277 0.42826 3.64964
31 5FA6 NAP 0.02331 0.42826 3.64964
32 4AT0 FAD 0.03561 0.40501 3.72549
33 4P8K 38C 0.03104 0.4095 3.75
34 1MH1 GNP 0.0103 0.4095 3.76344
35 1RYO OXL 0.0264 0.40485 3.97554
36 3GJX GTP 0.01524 0.40158 4.0146
37 1MOQ GLP 0.00953 0.40119 4.07609
38 1CZR FMN 0.001108 0.44318 4.14201
39 5AYV KPL 0.02122 0.40559 4.20712
40 2WC1 FMN 0.002123 0.41177 4.3956
41 4CP8 MLI 0.01294 0.41396 4.51745
42 2XTZ GSP 0.01117 0.40786 4.51977
43 4JLS 3ZE 0.02215 0.40184 4.60526
44 1ZUA TOL 0.04887 0.40153 4.73186
45 1ZUA NAP 0.04887 0.40153 4.73186
46 2PS1 ORO 0.008441 0.41592 4.86726
47 3M1I GTP 0.01212 0.4062 5.02283
48 2VVM FAD 0.03174 0.40181 5.05051
49 4UP3 FAD 0.006114 0.43692 5.09554
50 5W8V 9YP 0.01264 0.4024 5.11628
51 3RGQ 5P5 0.00615 0.42998 5.12821
52 2ZE7 DST 0.008234 0.41402 5.13834
53 1UI0 URA 0.007871 0.42226 5.36585
54 1JJ7 ADP 0.01552 0.41148 5.38462
55 2Q9U FMN 0.002977 0.40533 5.55556
56 3MBI HSX 0.01154 0.40927 5.57491
57 5UWS GNP 0.006166 0.42133 5.59441
58 5UWP GNP 0.01039 0.41074 5.59441
59 5UWR GNP 0.01093 0.40831 5.59441
60 1SVK ALF GDP 0.01423 0.407 5.66572
61 4BMO FMN 0.009776 0.41055 5.90062
62 1N62 FAD 0.02267 0.40717 6.0241
63 1DQN IMU 0.01745 0.40042 6.08696
64 5K9B FMN 0.0009946 0.44529 6.11111
65 1AG9 FMN 0.001063 0.444 6.28571
66 3KJS DQ1 0.03166 0.40187 6.33397
67 1RL4 BRR 0.004962 0.43231 6.38298
68 2OG2 MLI 0.02808 0.4114 6.40669
69 3RC3 ANP 0.01394 0.40523 6.56934
70 1IG3 VIB 0.01567 0.40822 6.84411
71 5J6Y BGC 0.006771 0.41973 6.91489
72 5J6Y GLC 0.006771 0.41973 6.91489
73 1X9I G6Q 0.005038 0.41772 6.95364
74 3H0L ADP 0.01189 0.40861 7.44681
75 3KAP FMN 0.003426 0.42498 7.48299
76 2XOD FMN 0.005246 0.41476 7.56302
77 4ZBY URA 0.0134 0.40853 7.73196
78 1B1C FMN 0.002141 0.41342 7.73481
79 2ODE ALF GDP 0.01613 0.40314 7.80142
80 5IXJ THR 0.001819 0.45045 8.33333
81 3AB4 THR 0.004019 0.43171 8.42697
82 3AB4 LYS 0.008032 0.40828 8.42697
83 1T57 FMN 0.00001426 0.53541 8.73786
84 3RK0 AMP 0.001491 0.42262 8.86076
85 5NUL FMN 0.002591 0.41497 10.1449
86 4P83 U5P 0.003118 0.43211 10.4396
87 2POC BG6 0.003088 0.42318 11.7166
88 1HGX 5GP 0.01064 0.41099 12.5683
89 3HGM ATP 0.00464 0.419 12.9252
90 3F6R FMN 0.002541 0.42493 15.5405
91 1FQK ALF 0.01497 0.40952 16.3265
92 3F81 STT 0.0009178 0.46457 16.3934
93 4HEQ FMN 0.002104 0.43069 17.8082
94 5WDR GNP 0.01644 0.40004 18.1287
95 4N82 FMN 0.002371 0.41686 18.5393
96 2JBH 5GP 0.01105 0.41019 20
97 2FCR FMN 0.0008811 0.44312 20.2312
Pocket No.: 3; Query (leader) PDB : 4B2D; Ligand: FBP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4b2d.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4B2D; Ligand: SER; 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: 4b2d.bio1) has 9 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 4B2D; Ligand: FBP; 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: 4b2d.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 4B2D; Ligand: FBP; 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: 4b2d.bio1) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 4B2D; Ligand: SER; Similar sites found: 28
This union binding pocket(no: 7) in the query (biounit: 4b2d.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3GXZ NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.004754 0.42548 None
2 3GXZ BMA MAN MAN MAN 0.009839 0.41473 None
3 3EYA FAD 0.009433 0.43904 1.45985
4 5BVA FAD 0.03541 0.42201 1.46699
5 3H4L ANP 0.01775 0.40197 1.90736
6 3OOI SAM 0.02595 0.40341 2.15517
7 1GUZ NAD 0.04802 0.40188 2.25806
8 1RP0 AHZ 0.02307 0.40882 3.16901
9 4LXQ TYD 0.02354 0.40719 3.28467
10 4LXQ FON 0.02354 0.40719 3.28467
11 4J5R A1R 0.02547 0.40549 3.42466
12 2E5A LAQ 0.04536 0.40837 3.45821
13 1FIQ SAL 0.03265 0.408 4.10959
14 1FIQ MTE 0.02995 0.408 4.10959
15 1PN0 FAD 0.0434 0.41484 5.29197
16 1PN0 IPH 0.04456 0.41484 5.29197
17 4J36 FAD 0.01534 0.43608 5.3012
18 4J36 1HR 0.02038 0.43608 5.3012
19 2P53 NNG 0.04081 0.40069 5.75916
20 3HP8 SUC 0.005686 0.41079 6.36364
21 3V91 UPG 0.02264 0.41865 7.90378
22 1F7K UMP 0.02397 0.40241 8.08823
23 2OL1 UMP 0.0186 0.41476 8.16327
24 2HQU DUP 0.02013 0.41882 8.53659
25 1SL4 MAN MAN MAN MAN 0.01256 0.41325 9.03226
26 1UP7 NAD 0.02166 0.41609 9.59233
27 4XJ7 ADN 0.008586 0.41521 14.6067
28 3F4F UMP 0.004028 0.44363 16.7665
Pocket No.: 8; Query (leader) PDB : 4B2D; Ligand: SER; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 4b2d.bio1) has 10 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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