FAIRMol

Z56900576

Pose ID 503 Compound 504 Pose 503

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
T01
Human DHFR Human
Ligand Z56900576
PDB5SD8↗

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
47.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.62, Jaccard 0.50, H-bond role recall 0.20
Burial
93%
Hydrophobic fit
75%
Reason: strain 47.0 kcal/mol
strain ΔE 47.0 kcal/mol 2 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.207 kcal/mol/HA) ✓ Good fit quality (FQ -10.97) ✓ Good H-bonds (5 bonds) ✓ Deep burial (93% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ Extreme strain energy (47.0 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-30.172
kcal/mol
LE
-1.207
kcal/mol/HA
Fit Quality
-10.97
FQ (Leeson)
HAC
25
heavy atoms
MW
358
Da
LogP
0.98
cLogP
Strain ΔE
47.0 kcal/mol
SASA buried
93%
Lipo contact
75% BSA apolar/total
SASA unbound
594 Ų
Apolar buried
416 Ų

Interaction summary

HB 5 HY 24 PI 1 CLASH 2
Final rank2.838Score-30.172
Inter norm-1.164Intra norm-0.043
Top1000noExcludedno
Contacts18H-bonds5
Artifact reasongeometry warning; 6 clashes; 2 protein clashes; high strain Δ 47.0
Residues
ALA10 ARG29 GLU31 ILE8 LEU23 LEU28 NAP201 PHE32 PHE35 PRO27 SER60 THR137 THR57 TRP25 TYR122 TYR34 VAL116 VAL9

Protein summary

200 residues
Protein targetT01Atoms3128
Residues200Chains2
Residue summaryLYS:374; LEU:361; GLU:240; VAL:224; ARG:192; PHE:180; ILE:171; PRO:168; ASN:140; SER:132; TYR:126; GLN:119; ASP:108; MET:102; THR:98; GLY:91

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:NAP201

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name5SD8Contacts21
PoseOpen native poseHB0
IFP residues
ALA10 ASN65 ASP22 GLN36 GLU31 GLY117 GLY21 ILE61 ILE8 LEU23 LEU68 NAP201 PHE32 PHE35 PRO62 SER60 THR137 THR57 TYR122 VAL116 VAL9
Current overlap13Native recall0.62
Jaccard0.50RMSD-
HB strict0Strict recall0.00
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

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

HY · Hydrophobic contacts

CLASH · Clashes

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
459 1.2720751774765935 -1.05921 -22.3772 5 17 0 0.00 0.00 - no Open
439 1.5054581612201845 -1.18078 -24.852 8 21 0 0.00 0.00 - no Open
503 2.8376502596628472 -1.16389 -30.1715 5 18 13 0.62 0.20 - 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 -30.172kcal/mol
Ligand efficiency (LE) -1.2069kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.971
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 25HA

Physicochemical properties
Molecular weight 358.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.98
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 47.00kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 74.33kcal/mol
Minimised FF energy 27.33kcal/mol

SASA & burial

✓ computed
SASA (unbound) 593.9Ų
Total solvent-accessible surface area of free ligand
BSA total 552.7Ų
Buried surface area upon binding
BSA apolar 416.4Ų
Hydrophobic contacts buried
BSA polar 136.4Ų
Polar contacts buried
Fraction buried 93.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 75.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1512.8Ų
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 1677.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 622.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)