FAIRMol

Z56815073

Pose ID 2010 Compound 318 Pose 655

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
T03
L. major DHFR L. major
Ligand Z56815073

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
36.0 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.75, Jaccard 0.65, H-bond role recall 0.20
Burial
90%
Hydrophobic fit
76%
Reason: 6 internal clashes
6 protein-contact clashes 6 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 (-1.003 kcal/mol/HA) ✓ Good fit quality (FQ -9.86) ✓ Deep burial (90% SASA buried) ✓ Lipophilic contacts well-matched (76%) ✗ Very high strain energy (36.0 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (9) ✗ Many internal clashes (12)
Score
-32.097
kcal/mol
LE
-1.003
kcal/mol/HA
Fit Quality
-9.86
FQ (Leeson)
HAC
32
heavy atoms
MW
569
Da
LogP
6.24
cLogP
Final rank
1.8474
rank score
Inter norm
-1.007
normalised
Contacts
18
H-bonds 3
Strain ΔE
36.0 kcal/mol
SASA buried
90%
Lipo contact
76% BSA apolar/total
SASA unbound
755 Ų
Apolar buried
516 Ų

Interaction summary

HBA 2 HY 9 PI 3 CLASH 6

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

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.
Name3CL9Contacts20
PoseOpen native poseHB0
IFP residues
ALA32 ARG97 ASP52 ILE45 LEU94 LYS57 MET53 NDP301 PHE56 PHE91 PRO88 SER86 THR180 THR54 THR83 TYR162 VAL156 VAL30 VAL31 VAL87
Current overlap15Native recall0.75
Jaccard0.65RMSD-
HB strict1Strict recall0.14
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

Protein summary

225 residues
Protein targetT03Atoms3428
Residues225Chains2
Residue summaryLEU:380; ARG:360; VAL:272; LYS:264; ALA:240; GLU:240; PRO:224; PHE:180; THR:154; ILE:152; SER:132; TYR:126; GLN:119; ASN:98; GLY:84; NDP:74

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:NDP301

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 1 0.05 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 15 0.75 0.20 - no Current
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 1 0.05 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 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 -32.097kcal/mol
Ligand efficiency (LE) -1.0030kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.864
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) 36.05kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -14.09kcal/mol
Minimised FF energy -50.14kcal/mol

SASA & burial

✓ computed
SASA (unbound) 754.8Ų
Total solvent-accessible surface area of free ligand
BSA total 675.9Ų
Buried surface area upon binding
BSA apolar 516.3Ų
Hydrophobic contacts buried
BSA polar 159.7Ų
Polar contacts buried
Fraction buried 89.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 76.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1587.1Ų
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 1820.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 806.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)