FAIRMol

Z56935326

Pose ID 9426 Compound 3820 Pose 618

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
T14
T. brucei ODC (G418 binding site) T. brucei G418 binding site
Ligand Z56935326
PDB1NJJ↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry medium Native mixed SASA done
Strain ΔE
20.0 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.53, Jaccard 0.40, H-bond role recall 0.40
Burial
66%
Hydrophobic fit
93%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes 82% of hydrophobic surface is solvent-exposed (27/33 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 ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.499 kcal/mol/HA) ✓ Good fit quality (FQ -5.08) ✓ Good H-bonds (5 bonds) ✓ Deep burial (66% SASA buried) ✓ Lipophilic contacts well-matched (93%) ✗ High strain energy (20.0 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (7) ✗ Many internal clashes (17)
Score
-17.978
kcal/mol
LE
-0.499
kcal/mol/HA
Fit Quality
-5.08
FQ (Leeson)
HAC
36
heavy atoms
MW
465
Da
LogP
8.45
cLogP
Strain ΔE
20.0 kcal/mol
SASA buried
66%
Lipo contact
93% BSA apolar/total
SASA unbound
820 Ų
Apolar buried
499 Ų

Interaction summary

HB 5 HY 2 PI 0 CLASH 4 ⚠ Exposure 81%
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
82% of hydrophobic surface is solvent-exposed (27/33 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 33 Buried (contacted) 6 Exposed 27 LogP 8.45 H-bonds 5
Exposed fragments: phenyl (3/5 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)
Final rank2.283Score-17.978
Inter norm-0.722Intra norm0.218
Top1000noExcludedno
Contacts13H-bonds5
Artifact reasongeometry warning; 17 clashes; 7 protein contact clashes; moderate strain Δ 20.0
Residues
ARG242 ARG337 ASP243 ASP385 ASP47 GLU384 LEU339 LYS51 MET386 PHE383 SER282 THR241 VAL336

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

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 overlap8Native recall0.53
Jaccard0.40RMSD-
HB strict1Strict recall0.17
HB same residue+role2HB role recall0.40
HB same residue2HB residue recall0.40

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

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

HY · Hydrophobic contacts

CLASH · Clashes

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
646 1.7156329818132328 -0.891214 -31.0983 4 20 0 0.00 0.00 - no Open
618 2.2834219032557037 -0.721979 -17.9781 5 13 8 0.53 0.40 - no Current
637 4.176813228467483 -0.807567 -23.4984 3 16 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 -17.978kcal/mol
Ligand efficiency (LE) -0.4994kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.076
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 36HA

Physicochemical properties
Molecular weight 464.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 8.45
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 20.00kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 106.85kcal/mol
Minimised FF energy 86.85kcal/mol

SASA & burial

✓ computed
SASA (unbound) 820.1Ų
Total solvent-accessible surface area of free ligand
BSA total 537.4Ų
Buried surface area upon binding
BSA apolar 499.3Ų
Hydrophobic contacts buried
BSA polar 38.1Ų
Polar contacts buried
Fraction buried 65.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 92.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2685.4Ų
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 1440.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)