FAIRMol

KB_HAT_183

Pose ID 8953 Compound 1900 Pose 145

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 KB_HAT_183
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
Promising but geometrically suspicious
Binding strong Geometry low Native mixed SASA done
Strain ΔE
46.0 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.47, Jaccard 0.33, H-bond role recall 0.20
Burial
75%
Hydrophobic fit
80%
Reason: strain 46.0 kcal/mol
strain ΔE 46.0 kcal/mol 3 protein-contact clashes 3 intramolecular clashes 79% of hydrophobic surface is solvent-exposed (15/19 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.
✓ Good LE (-0.313 kcal/mol/HA) ✓ Good fit quality (FQ -3.02) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (75% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Extreme strain energy (46.0 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (8) ✗ Many internal clashes (13)
Score
-9.400
kcal/mol
LE
-0.313
kcal/mol/HA
Fit Quality
-3.02
FQ (Leeson)
HAC
30
heavy atoms
MW
413
Da
LogP
3.91
cLogP
Final rank
2.0624
rank score
Inter norm
-0.738
normalised
Contacts
13
H-bonds 8
Strain ΔE
46.0 kcal/mol
SASA buried
75%
Lipo contact
80% BSA apolar/total
SASA unbound
649 Ų
Apolar buried
389 Ų

Interaction summary

HBA 6 HY 2 PI 0 CLASH 3

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

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
Jaccard0.33RMSD-
HB strict0Strict recall0.00
HB same residue+role1HB role recall0.20
HB same residue2HB residue recall0.40

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
145 2.0624180278032496 -0.737854 -9.39962 8 13 7 0.47 0.20 - no Current
61 2.3969608717699287 -0.94498 -22.331 5 14 0 0.00 0.00 - no Open
90 3.905882627218545 -0.962538 -28.5081 10 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 -9.400kcal/mol
Ligand efficiency (LE) -0.3133kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -3.022
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 413.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.91
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 45.96kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -33.14kcal/mol
Minimised FF energy -79.10kcal/mol

SASA & burial

✓ computed
SASA (unbound) 648.8Ų
Total solvent-accessible surface area of free ligand
BSA total 489.2Ų
Buried surface area upon binding
BSA apolar 388.8Ų
Hydrophobic contacts buried
BSA polar 100.4Ų
Polar contacts buried
Fraction buried 75.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2456.9Ų
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 1425.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)