FAIRMol

Z56905026

Pose ID 8684 Compound 964 Pose 554

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
T13
T. brucei ODC (Active site) T. brucei Active site
Ligand Z56905026
PDB1F3T↗

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 strong SASA done
Strain ΔE
45.1 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.74, Jaccard 0.61, H-bond role recall 0.43
Burial
78%
Hydrophobic fit
78%
Reason: strain 45.1 kcal/mol
strain ΔE 45.1 kcal/mol 1 protein-contact clashes 35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Not classified (>100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low Ames Clear DILI Low
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.079 kcal/mol/HA) ✓ Good fit quality (FQ -9.94) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ Extreme strain energy (45.1 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (9) ✗ Internal clashes (6)
Score
-28.063
kcal/mol
LE
-1.079
kcal/mol/HA
Fit Quality
-9.94
FQ (Leeson)
HAC
26
heavy atoms
MW
376
Da
LogP
0.44
cLogP
Final rank
1.1635
rank score
Inter norm
-1.115
normalised
Contacts
18
H-bonds 8
Strain ΔE
45.1 kcal/mol
SASA buried
78%
Lipo contact
78% BSA apolar/total
SASA unbound
613 Ų
Apolar buried
371 Ų

Interaction summary

HBD 3 HBA 5 HY 3 PI 3 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

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.
Name1F3TContacts19
PoseOpen native poseHB0
IFP residues
ALA111 ALA67 ARG154 ARG277 ASP332 ASP88 CYS70 GLU274 GLY236 GLY237 GLY276 HIS197 LYS69 PHE238 PRO275 SER200 TYR278 TYR331 TYR389
Current overlap14Native recall0.74
Jaccard0.61RMSD-
HB strict4Strict recall0.44
HB same residue+role3HB role recall0.43
HB same residue4HB residue recall0.57

Protein summary

411 residues
Protein targetT13Atoms6340
Residues411Chains1
Residue summaryVAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
554 1.1634603475701728 -1.11522 -28.0629 8 18 14 0.74 0.43 - no Current
548 1.3240072850088074 -0.975344 -21.3145 8 18 0 0.00 0.00 - no Open
567 2.7646106793291505 -1.09795 -24.8055 8 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 -28.063kcal/mol
Ligand efficiency (LE) -1.0793kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.944
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 376.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.44
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 45.07kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 98.31kcal/mol
Minimised FF energy 53.23kcal/mol

SASA & burial

✓ computed
SASA (unbound) 613.2Ų
Total solvent-accessible surface area of free ligand
BSA total 476.2Ų
Buried surface area upon binding
BSA apolar 371.1Ų
Hydrophobic contacts buried
BSA polar 105.1Ų
Polar contacts buried
Fraction buried 77.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 77.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2539.0Ų
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 3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1388.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)