FAIRMol

MK47

Pose ID 8314 Compound 584 Pose 184

DB SELECTIONDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T13
T. brucei ODC (Active site) T. brucei Active site
Ligand MK47
PDB1F3T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
23.5 kcal/mol
Protein clashes
7
Internal clashes
4
Native overlap
contact recall 0.68, Jaccard 0.54, H-bond role recall 0.57
Burial
77%
Hydrophobic fit
58%
Reason: no major geometry red flags detected
7 protein-contact clashes 4 intramolecular clashes 62% of hydrophobic surface is solvent-exposed (10/16 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.335 kcal/mol/HA) ✓ Good fit quality (FQ -11.96) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (77% SASA buried) ✗ High strain energy (23.5 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (7)
Score
-32.041
kcal/mol
LE
-1.335
kcal/mol/HA
Fit Quality
-11.96
FQ (Leeson)
HAC
24
heavy atoms
MW
367
Da
LogP
3.19
cLogP
Final rank
0.3144
rank score
Inter norm
-1.406
normalised
Contacts
18
H-bonds 12
Strain ΔE
23.5 kcal/mol
SASA buried
77%
Lipo contact
58% BSA apolar/total
SASA unbound
605 Ų
Apolar buried
269 Ų

Interaction summary

HBD 2 HBA 6 HY 3 PI 2 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 6.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
No clash · clashes detected for this pose.

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name1F3TContacts19
PoseOpen native poseHB0
IFP residues
ALA111 ALA67 ARG154 ARG277 ASP332 ASP88 CYS70 GLU274 GLY236 GLY237 GLY276 HIS197 LYS69 PHE238 PRO275 SER200 TYR278 TYR331 TYR389
Current overlap13Native recall0.68
Jaccard0.54RMSD-
HB strict5Strict recall0.56
HB same residue+role4HB role recall0.57
HB same residue5HB residue recall0.71

Protein summary

411 residues
Protein targetT13Atoms6340
Residues411Chains1
Residue summaryVAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
184 0.31439389166778003 -1.40551 -32.0406 12 18 13 0.68 0.57 - no Current
285 0.7378236916649001 -1.07057 -19.17 10 13 0 0.00 0.00 - no Open
264 1.832378261869399 -1.13636 -21.5369 11 18 0 0.00 0.00 - no Open
324 3.4984978735652543 -1.15564 -23.385 4 11 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -32.041kcal/mol
Ligand efficiency (LE) -1.3350kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.964
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 366.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.19
Lipinski: ≤ 5
Rotatable bonds 10

Conformational strain (MMFF94s)
Strain energy (ΔE) 23.51kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 34.49kcal/mol
Minimised FF energy 10.99kcal/mol

SASA & burial

✓ computed
SASA (unbound) 605.5Ų
Total solvent-accessible surface area of free ligand
BSA total 465.9Ų
Buried surface area upon binding
BSA apolar 268.5Ų
Hydrophobic contacts buried
BSA polar 197.4Ų
Polar contacts buried
Fraction buried 76.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 57.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2476.4Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1370.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)