FAIRMol

Z56815073

Pose ID 8796 Compound 318 Pose 666

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
T13
T. brucei ODC (Active site) T. brucei Active site
Ligand Z56815073
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
58.0 kcal/mol
Protein clashes
9
Internal clashes
9
Native overlap
contact recall 0.89, Jaccard 0.74, H-bond role recall 0.71
Burial
78%
Hydrophobic fit
68%
Reason: 9 protein-contact clashes, 9 internal clashes, strain 58.0 kcal/mol
strain ΔE 58.0 kcal/mol 9 protein-contact clashes 9 intramolecular clashes
EcoTox / ADMET GDS: UNSAFE UL GreenDrugScore ML model
ECOscore
0.282
aquatic tox · BCF · biodeg.
GDS₃ (3-block)
0.393
ADMET + ECO + DL
ADMETscore (GDS)
0.430
absorption · distr. · metab.
DLscore
0.396
drug-likeness
P(SAFE)
0.05
GDS classification
ADMET alerts (in-silico)
hERG High Ames Clear DILI Risk
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.723 kcal/mol/HA) ✓ Good fit quality (FQ -7.11) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ Extreme strain energy (58.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-23.136
kcal/mol
LE
-0.723
kcal/mol/HA
Fit Quality
-7.11
FQ (Leeson)
HAC
32
heavy atoms
MW
569
Da
LogP
6.24
cLogP
Final rank
5.2975
rank score
Inter norm
-0.919
normalised
Contacts
21
H-bonds 13
Strain ΔE
58.0 kcal/mol
SASA buried
78%
Lipo contact
68% BSA apolar/total
SASA unbound
677 Ų
Apolar buried
358 Ų

Interaction summary

HBD 1 HBA 7 HY 5 PI 4 CLASH 9

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 7.

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 overlap17Native recall0.89
Jaccard0.74RMSD-
HB strict6Strict recall0.67
HB same residue+role5HB role recall0.71
HB same residue5HB residue recall0.71

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
662 0.6661725537921506 -1.04002 -28.6522 3 19 0 0.00 0.00 - no Open
659 0.7707737947628458 -0.753505 -21.1708 0 16 0 0.00 0.00 - no Open
652 0.8225922751736459 -1.01993 -29.9798 1 17 0 0.00 0.00 - no Open
642 1.139808952940768 -0.847734 -26.7285 5 14 0 0.00 0.00 - no Open
656 1.7653889637304623 -0.867492 -24.6089 3 18 0 0.00 0.00 - no Open
655 1.8473635475241321 -1.0072 -32.0974 3 18 0 0.00 0.00 - no Open
638 1.9648568381193203 -0.927569 -29.9449 4 16 0 0.00 0.00 - no Open
645 2.1923496622071084 -0.758001 -17.56 2 18 0 0.00 0.00 - no Open
661 2.2567473265764555 -0.765666 -25.1725 7 20 0 0.00 0.00 - no Open
641 2.292373942513122 -0.725642 -22.2969 4 13 0 0.00 0.00 - no Open
641 2.2974884616866427 -0.933418 -28.8424 4 19 0 0.00 0.00 - no Open
654 3.071439811116401 -0.870778 -29.2301 13 16 0 0.00 0.00 - no Open
659 3.8692944863611776 -0.656079 -21.7278 6 10 0 0.00 0.00 - no Open
660 3.931763085408765 -0.81696 -27.3427 3 19 0 0.00 0.00 - no Open
666 5.297500006745246 -0.919049 -23.1364 13 21 17 0.89 0.71 - 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 -23.136kcal/mol
Ligand efficiency (LE) -0.7230kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.110
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 32HA

Physicochemical properties
Molecular weight 568.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 6.24
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 58.01kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 10.62kcal/mol
Minimised FF energy -47.39kcal/mol

SASA & burial

✓ computed
SASA (unbound) 677.0Ų
Total solvent-accessible surface area of free ligand
BSA total 527.6Ų
Buried surface area upon binding
BSA apolar 358.0Ų
Hydrophobic contacts buried
BSA polar 169.6Ų
Polar contacts buried
Fraction buried 77.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 67.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2538.5Ų
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 1430.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)