FAIRMol

MK172A

Pose ID 9109 Compound 3232 Pose 301

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 MK172A
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 medium Native mixed SASA done
Strain ΔE
17.2 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.47, Jaccard 0.29, H-bond role recall 0.00
Burial
72%
Hydrophobic fit
80%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes 100% of hydrophobic surface is solvent-exposed (28/28 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 (-0.841 kcal/mol/HA) ✓ Good fit quality (FQ -8.42) ✓ Good H-bonds (5 bonds) ✓ Deep burial (72% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Moderate strain (17.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (23)
Score
-28.607
kcal/mol
LE
-0.841
kcal/mol/HA
Fit Quality
-8.42
FQ (Leeson)
HAC
34
heavy atoms
MW
473
Da
LogP
5.68
cLogP
Final rank
5.7390
rank score
Inter norm
-0.741
normalised
Contacts
16
H-bonds 6
Strain ΔE
17.2 kcal/mol
SASA buried
72%
Lipo contact
80% BSA apolar/total
SASA unbound
727 Ų
Apolar buried
423 Ų

Interaction summary

HBD 1 HBA 4 HY 0 PI 0 CLASH 4

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.

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

HY · Hydrophobic contacts
No hy · hydrophobic contacts detected for this pose.

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 overlap7Native recall0.47
Jaccard0.29RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
233 1.7169251309642504 -0.805564 -23.8966 6 14 0 0.00 0.00 - no Open
221 3.6210576690556837 -0.965332 -33.6248 8 17 0 0.00 0.00 - no Open
256 4.491988375451721 -0.717114 -20.3939 4 15 0 0.00 0.00 - no Open
301 5.738961216462839 -0.741369 -28.6065 6 16 7 0.47 0.00 - no Current

Molecular metrics

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

Scoring & efficiency
Docking score -28.607kcal/mol
Ligand efficiency (LE) -0.8414kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.419
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 34HA

Physicochemical properties
Molecular weight 472.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.68
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 17.18kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 80.82kcal/mol
Minimised FF energy 63.64kcal/mol

SASA & burial

✓ computed
SASA (unbound) 727.2Ų
Total solvent-accessible surface area of free ligand
BSA total 527.6Ų
Buried surface area upon binding
BSA apolar 422.8Ų
Hydrophobic contacts buried
BSA polar 104.8Ų
Polar contacts buried
Fraction buried 72.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2578.3Ų
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 1390.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)