FAIRMol

MK221

Pose ID 9123 Compound 649 Pose 315

DB fairmolDocking 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
T14
T. brucei ODC (G418 binding site) T. brucei G418 binding site
Ligand MK221
PDB1NJJ↗

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 high Native strong SASA done
Strain ΔE
20.9 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.80, Jaccard 0.63, H-bond role recall 0.40
Burial
75%
Hydrophobic fit
81%
Reason: no major geometry red flags detected
1 protein-contact clashes 73% of hydrophobic surface is solvent-exposed (19/26 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 (-0.619 kcal/mol/HA) ✓ Good fit quality (FQ -6.14) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (75% SASA buried) ✓ Lipophilic contacts well-matched (81%) ✗ High strain energy (20.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-20.435
kcal/mol
LE
-0.619
kcal/mol/HA
Fit Quality
-6.14
FQ (Leeson)
HAC
33
heavy atoms
MW
452
Da
LogP
4.67
cLogP
Final rank
3.3239
rank score
Inter norm
-0.726
normalised
Contacts
16
H-bonds 11
Strain ΔE
20.9 kcal/mol
SASA buried
75%
Lipo contact
81% BSA apolar/total
SASA unbound
792 Ų
Apolar buried
479 Ų

Interaction summary

HBD 1 HBA 5 HY 3 PI 0 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name1NJJContacts15
PoseOpen native poseHB0
IFP residues
ARG22 ARG242 ARG337 ARG342 ASP243 ASP385 GLN341 GLU384 LEU25 LEU339 LEU382 PRO340 PRO344 SER282 THR241
Current overlap12Native recall0.80
Jaccard0.63RMSD-
HB strict2Strict recall0.33
HB same residue+role2HB role recall0.40
HB same residue3HB residue recall0.60

Protein summary

398 residues
Protein targetT14Atoms6140
Residues398Chains1
Residue summaryVAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:ORX602

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
268 0.974102900606285 -0.753355 -22.1827 4 20 0 0.00 0.00 - no Open
275 2.048310136114584 -0.934394 -26.071 5 15 0 0.00 0.00 - no Open
315 3.3238944949654337 -0.72587 -20.4346 11 16 12 0.80 0.40 - no Current
291 3.5287369862351285 -0.96868 -26.5329 9 18 0 0.00 0.00 - no Open
314 3.6667135220935343 -0.697525 -18.9353 6 19 0 0.00 0.00 - no Open
211 4.016080999071254 -0.860195 -23.0569 14 18 0 0.00 0.00 - no Open
218 4.624022710023361 -0.952362 -25.0393 11 18 0 0.00 0.00 - no Open
322 4.667651235211368 -0.611785 -19.6032 8 14 0 0.00 0.00 - no Open
341 4.781422519779941 -0.793315 -20.1332 4 20 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 -20.435kcal/mol
Ligand efficiency (LE) -0.6192kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.144
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 451.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.67
Lipinski: ≤ 5
Rotatable bonds 10

Conformational strain (MMFF94s)
Strain energy (ΔE) 20.89kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 43.14kcal/mol
Minimised FF energy 22.25kcal/mol

SASA & burial

✓ computed
SASA (unbound) 792.5Ų
Total solvent-accessible surface area of free ligand
BSA total 591.5Ų
Buried surface area upon binding
BSA apolar 478.6Ų
Hydrophobic contacts buried
BSA polar 113.0Ų
Polar contacts buried
Fraction buried 74.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2628.4Ų
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 3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1385.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)