FAIRMol

Z56779217

Pose ID 9180 Compound 4213 Pose 372

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 Z56779217
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 mixed SASA done
Strain ΔE
14.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.40, Jaccard 0.29, H-bond role recall 0.20
Burial
74%
Hydrophobic fit
86%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.003 kcal/mol/HA) ✓ Good fit quality (FQ -8.56) ✓ Good H-bonds (3 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (86%) ✗ Moderate strain (14.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-21.069
kcal/mol
LE
-1.003
kcal/mol/HA
Fit Quality
-8.56
FQ (Leeson)
HAC
21
heavy atoms
MW
298
Da
LogP
4.45
cLogP
Final rank
3.6767
rank score
Inter norm
-1.084
normalised
Contacts
12
H-bonds 4
Strain ΔE
14.7 kcal/mol
SASA buried
74%
Lipo contact
86% BSA apolar/total
SASA unbound
508 Ų
Apolar buried
325 Ų

Interaction summary

HBD 1 HBA 2 HY 4 PI 0 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

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 overlap6Native recall0.40
Jaccard0.29RMSD-
HB strict0Strict recall0.00
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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
372 3.6767328210226413 -1.08405 -21.0692 4 12 6 0.40 0.20 - 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 -21.069kcal/mol
Ligand efficiency (LE) -1.0033kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.558
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 21HA

Physicochemical properties
Molecular weight 297.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.45
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 14.66kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 58.47kcal/mol
Minimised FF energy 43.81kcal/mol

SASA & burial

✓ computed
SASA (unbound) 508.5Ų
Total solvent-accessible surface area of free ligand
BSA total 376.1Ų
Buried surface area upon binding
BSA apolar 325.3Ų
Hydrophobic contacts buried
BSA polar 50.8Ų
Polar contacts buried
Fraction buried 74.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 86.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2407.6Ų
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 1399.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)