FAIRMol

Z31076755

Pose ID 8650 Compound 2667 Pose 520

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 Z31076755
PDB1F3T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry high Native strong SASA done
Strain ΔE
12.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.63, Jaccard 0.60, H-bond role recall 0.57
Burial
76%
Hydrophobic fit
65%
Reason: no major geometry red flags detected
1 protein-contact clashes
EcoTox / ADMET GDS: UNSAFE UL GreenDrugScore ML model
ECOscore
0.282
aquatic tox · BCF · biodeg.
GDS₃ (3-block)
0.385
ADMET + ECO + DL
ADMETscore (GDS)
0.408
absorption · distr. · metab.
DLscore
0.408
drug-likeness
P(SAFE)
0.39
GDS classification
ADMET alerts (in-silico)
hERG Low Ames Clear DILI Low
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.304 kcal/mol/HA) ✓ Good fit quality (FQ -11.32) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (76% SASA buried) ✓ Lipophilic contacts well-matched (65%) ✗ Moderate strain (12.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-28.697
kcal/mol
LE
-1.304
kcal/mol/HA
Fit Quality
-11.32
FQ (Leeson)
HAC
22
heavy atoms
MW
347
Da
LogP
3.47
cLogP
Final rank
3.4185
rank score
Inter norm
-1.324
normalised
Contacts
13
H-bonds 12
Strain ΔE
12.3 kcal/mol
SASA buried
76%
Lipo contact
65% BSA apolar/total
SASA unbound
512 Ų
Apolar buried
253 Ų

Interaction summary

HBA 9 HY 2 PI 3 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.

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 overlap12Native recall0.63
Jaccard0.60RMSD-
HB strict5Strict recall0.56
HB same residue+role4HB role recall0.57
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
503 -0.412716455525595 -1.4097 -27.6491 1 15 0 0.00 0.00 - no Open
539 1.74159394392578 -1.15122 -25.5295 8 17 0 0.00 0.00 - no Open
517 2.6126169913137653 -1.21113 -26.8425 4 13 0 0.00 0.00 - no Open
520 3.4185448372354834 -1.32408 -28.697 12 13 12 0.63 0.57 - 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 -28.697kcal/mol
Ligand efficiency (LE) -1.3044kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.325
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 22HA

Physicochemical properties
Molecular weight 346.8Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.47
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 12.31kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 11.05kcal/mol
Minimised FF energy -1.26kcal/mol

SASA & burial

✓ computed
SASA (unbound) 511.7Ų
Total solvent-accessible surface area of free ligand
BSA total 390.7Ų
Buried surface area upon binding
BSA apolar 253.1Ų
Hydrophobic contacts buried
BSA polar 137.5Ų
Polar contacts buried
Fraction buried 76.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 64.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2379.2Ų
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 1401.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)